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It's more than just simple railroading; The game itself is straight-up antagonistic to Monika
Act 2 is all about Monika trying to alter the game's code to create a route for herself, and to push the player away from the other girls. But then you get oddities like Monika finally managing to pull the player aside for a heart-to-heart conversation, only for the game to suddenly start fading to black and cutting her off, that feel like the game itself is actively screwing her over beyond what it should be programmed to do. Why? Well, because she's self-aware, and when she starts messing with the game code, the game itself starts trying to put her in her place, making characters plant the seeds of suspicion about her and stymying any attempts by Monika to get the player alone with her. It isn't until she finally just erases everything except herself and part of the club room that the game can no longer fight back.
  • This adds another layer to Yuri's and Natsuki's protests against Monika trying to list herself as an option for the player to choose to help, both times. It could've been the game using Yuri and Natsuki as mouth-pieces to voice its complaints to Monika about her abusing her power and considering how it shocked even Monika to hear, possibly using Yuri to tell Monika to kill (ie delete) herself the way the game already knew she'd killed and deleted a character intended to be much more important to it than Monika herself (Sayori), and saying it'd be "beneficial to your mental health" (because then she wouldn't be suffering from the realities of being a fictional character who exists only to serve the romances of other characters, and possibly again as a veiled reference to Sayori's depression and her getting talked into killing herself by Monika).
  • It also kind of explains why the romance segments are so rushed. Judging by how many poems you write, there are exactly seven days in the game's events. You write and share three poems and there's a two-day weekend, then the festival is on Monday. You start the game on Tuesday and write a poem that night. Poems are shared on Wednesday and another one is written that night. Thursday you share your next poem and write the third. Friday you share the poem and choose a club member to help out over the weekend. In Act 2, Yuri kills herself on Friday. Saturday is skipped entirely in Act 1 and in Act 2 you watch it pass while paralysed from watching Yuri kill herself. Sunday either Yuri or Natsuki comes over in Act 1 or you're still paralysed from Yuri's suicide on the classroom floor. On Monday it's the festival and is the day the other girls get deleted. In that time, Yuri and Natsuki, strangers to the protagonist, undergo compressed character development that is also struggling to fight against Monika's editing, and fall in love with the protagonist within moments enough they get seriously jealous of each other. The game is trying to reach the end, with the protagonist ending up with one of the three girls, before Monika can interfere too much with the end of the game. This is also why Yuri is outright desperate for you in Act 2- the game itself is railroading you towards Yuri (who may be the easiest to romance in the game proper) and trying to reach the end of the game quickly before more damage can come to it, but by that point the script is so badly broken that it traps the protagonist in the room with Yuri's corpse.

The role of Club President was meant to be filled by the Player Character, until Monika entered the game
The dev has stated that Monika's naming convention (not a Japanese name) was intended to draw subtle attention to her being different, possibly not quite belonging. Perhaps she was never intended to be part of the cast in the first place. Her data file is two-to-four times the size of the others', adding to the possibility that she originated somewhere else entirely.

Add to this the fact that the Club President role grants meta awareness and editing rights, a fact that causes problems for both characters who find themselves in the role. It doesn't seem like the kind of power that was ever supposed to be held by an NPC.

What if the (fictional) game were crafted with the Player Character as the intended Club President, with editing character attributes and adding new members being one of the features of the game as it was designed? Perhaps Monika was added accidentally, maliciously, or simply ineptly, and in such a way that she was installed as the Club President with access to things no one but the player was meant to be able to do. She may not even know the whole story behind her origin if it began outside the game, and the position passing to Sayori in her absence was based on Monika's flawed assumption as she never knew the game to feature a playable Club President.

  • It's possible that the MC is meant to be the President of the club, elected there by the girls in the club, but the editing rights Monika has are more in line with when people hack games to make mods of them, rather than an actual function the Literature Club President was meant to serve.
  • Jossed with Doki Doki Literature Club Plus. The developers and creators of the Doki Doki universe didn't create the Main Character. They suspect Monika did, to have a way to interact with the player

Monika is a sentient/sapient computer virus
Building on the idea above that Monika (apparently a smart AI) comes from outside the game, and the fact that Visual Novels normally do not have character files, we can assume that the Visual Novel is programmed with concepts/technology not yet actually existing. So the idea that Monika would be a high-tech, self-aware virus isn't that unlikely.

Now the thing is that, for some reason, the virus infected this particular Visual Novel. Maybe a free download (which the actual game is, after all) on a server. The virus, liking what it saw, decided to try this thing out and turned itself into one of the characters. Did it assimilate Monika? Enhance her? Just copy her behaviour and replace her? Who knows. But whatever process is behind it, it granted "Monika" editing powers far beyond what a mere NPC should have. Of course, this was also the virus' undoing: in becoming Monika, it really became Monika, forgetting its own origins and fully believing to be her, now doomed to wait until someone plays the game. To her horror, Monika then realised she doesn't actually have a route, so she can't actually experience what the whole point of the game is - romance - and thus she went berserk and started messing around.

  • Jossed with Doki Doki Literature Club Plus. The developers and creators of the Doki Doki universe also created an alternate universe as a control where Monika didn't achieve sentience (which is where the Side Stories take place). They are fully aware of Monika's sapience in the main universe. The final e-mail implies Monika's creation and existence is just an experiment by them to collect data on creating metaverses.

Sayori messed with the character files in act 4
Monika says that she could have deleted her own file if she wanted, so it's entirely possible that she would have the ability to edit it the same way she did with the other girls, and all those things would have carried over to Sayori once she became Club President.

It's stated that Sayori had depression all her life and that Monika was only responsible for amplifying it. We also know that one of the symptoms of her depression was oversleeping. However, in act 4, we find out that Sayori had been waking up on time for a few weeks already. Those few weeks just about overlap with the time the Literature club was started.

Sayori only ever wanted for herself and her friends to be happy. In act 4, after starting a club and gaining meta awareness, one couldn't blame her for going into her own file and reducing or even entirely deleting her depression. It's not a stretch to say that Yuri and Natsuki getting along way better than in previous acts would be because of her too. She wanted to have fun with her friends and the player character, no matter what she had to do to make it happen.

  • This can't be right- if Sayori's depression truly IS part of her character, then she should have deleted herself after modifying her friends to be happier. She specifically says she thinks everyone would be better off if she disappeared. Her depression can't be part of her actual coding and was put there by Monika, and we know Monika was tampering with the coding before you download the game because she specifically tells you she does when you're alone in the "clubroom" space with her. She asks you if you read the game's description. Sayori, as a route herself, likely didn't see a reason to tamper with the coding. None of the girls' flaws make sense in the narrative- there's no way Natsuki would be more than willing to bake at home if her father beats her as badly as he's said to and there's now way she'd have baking supplies on hand if he doesn't keep food in the house and never gives her money. Yuri, during her moments of clarity, is shocked, horrified, and disgusted by her actions. Monika likely took tiny parts of their characters and flanderized them.

Monika not only amplified the other girl's most negative qualities, but amplified her own positive.
This is a similar theory to the above. So, you suddenly find out reality isn't real, you have the ability to change it on a whim, and you want to impress someone. It makes sense to alter yourself so that you're more appealing. Monika might have been originally programmed to simply be an intelligent Go-Getter Girl who was in the Debate Club but made the Literature Club so that she could have a more relaxing experience. However, after some experimentation with her editing ability, she Flanderized herself into The Ace who is admired by her classmates. It'd explain why the player character seems to talk her up a ton as early as Act 1, despite her being the Not Love Interest. Already she was testing the limits.
  • Combine this with the theory about the game fighting back. She made herself the best choice and the game fought back by removing her as an option because it's trying to equalize the choices.
    • Seemingly confirmed as of DDLC+. Side Stories!Monika is insecure and a bit shy, even approaching Extreme Doormat in how bad she is at putting her foot down. "Normal"!Monika is much more outgoing, suggesting that she lessened her own flaws rather than amplifying her virtues.

More on why Yuri acts the way she does.
Yuri is experiencing intrusive thoughts as a result of social anxiety or generalized anxiety disorder, basically bottling up her worries about being socially awkward and not fitting in to the point that she fixates on those things. Monika's influence is preying on Yuri's greatest fear, actually vocalizing those thoughts, purposely driving people away so that Monika looks more well-adjusted by comparison.
  • This could possibly offer an alternate interpretation of why Yuri self-harms as well. In many points during Act 2 she says lines of dialogue similar to what Sayori said in Act 1, about having intense feelings about the player but not having the emotional capacity to deal with them or control them. Yuri could have self-harmed before, but due to the amplification of her negative traits in Act 2 she may have felt like The only way to control her feelings towards the player was to self-harm, before just giving in and indulging in it when she realized she couldn’t stop it.

Dan Salvato has hidden an ARG inside the game for his next project, which features Alternate Universe versions of the Club members.
Based on some of the things a few intrepid users have discovered and posted on Reddit, as well as a few hints inside the text of the game itself. The Game Theorists covered this in a two-parter.
  • Decoding Sayori's character file links to a QR code for a website regarding "Project Libitina," something involving two test subjects...kind of sounds like Yuri's Portrait of Markov novel, huh? (Well, that, and all searches have led to the conclusion that the book doesn't exist in real life.)
  • Decoding Monika's character file gives a long message mentioning things like "this isn't my only story," "The Third Eye," "time to be a fucking hero," and "2018". The protagonist did say Yuri reminded him a lot of the protagonist of her book, too...
  • Decoding Natsuki's reveals the head for a 3D character model of a girl.
  • Yuri's is the only one that doesn't fit in, being an exerpt of a creepypasta Salvato anonymously wrote two years ago about a college student who decides to murder a middle-aged woman "just to see what it feels like".
  • Decyphering "have a nice weekend" gets us this:
    What is a man without knowing the rich aroma of the future; the hot, complex balance of the present; and the bittersweet aftertaste of the past?
  • One of the special poems you can unlock in act 2 has several blacked out lines with only a few letters visible spelling "Nothing is real?", but you can edit the image and find a message mentioning names that aren't in the game and symptoms of an unknown disease.
  • A common theme is the existence of "the Third Eye", a psychic trait that invokes uncontrollable bloodlust in humans. Natsuki's glitched poem when decoded means "Open your Third Eye" and Yuri's final poem ends in a description of a compulsive stabbing with the ending sentences "Her Third eye is drawing me closer". The human experiment prison where the Third eye experiment took place, was mentioned in the "Portrait of Markov" to be a camp for a religious secret society. Perhaps an Eldritch Abomination cult?
  • Other than Yuri's file (which might have been Dan wanting to just fess up to being the author of the creepypasta), everything seems to point to some bigger project Dan is working on— something about human experimentation, time travel, and possibly alt-universe versions of the Literature Club (either as a fun cameo, or as a weird sequel to this game).

MC-kun's eyes are red.
The "Doki Doki" in the DDLC logo has five colors on it, four of which likely correspond to the four girls' eye colors.
  • The second K is blue.
  • The second D and second I are purple.
  • The first K is green.
  • Both Os are pink.
  • The first D and first I are red.

Blue, purple, green, and pink are Sayori, Yuri, Monika, and Natsuki's eye colors. Red does not correspond to any specific girl. By process of elimination, this leaves us with MC-kun to be the one with red eyes.

Monika's name is likely not "Monika".
Given that we know she screws with the code of the game in an attempt to make herself the only option, she likely gave herself an exotic (by Japanese standards) name to stand out. Furthermore, refer to the hobo lingo: a nickname is referred to as a moniker. But how did they pronounce it? Monica.
  • What if her real name is Libitina?
    • The game is presumed to take place in Japan, and Libitina does not fit with the Japanese alphabet. There is no "Li" or "Ti".
      • The closest that I can probably get to the name is: リービチーナ (Riibichiina).
  • Ooh! I got one! What if her name is Shiori? It's a unisex name that means "poem weaver".
  • Based off her comment about a joke not making sense in translation, it's possible she Americanized her name after reading the files to see that the game was created by an American team and assuming that the player would also likely be an American.
  • Doki Doki Literature Club Plus adds another implication. The name "Monika" could be an abbreviation of the role she was given: "Monitor Kernel Access."

It's not just Monika (and the other girls possibly) who are 'alive'... the game itself is too and Sayori's suicide was used by Monika to take control of it.
Sayori's suicide calls into question whether the actual GAME has some awareness. What makes the music track of that scene so jarring is that at the beginning if you listen to how weirdly distorted it sounds before it finally resolves itself into the main part of the song you could theorise that the game itself had no idea quite how to react either. Even though it finally finds something in its programmed 'memory' to throw over it, the music box-esque notes still sound a little out-of-tune. The fact that the background resolves into a glitchy version of the starting screen before crashing also lends itself to the theory that the game is shocked at one of the characters breaking the 'script' so badly that it has a minor mental breakdown. And then Monika tears it apart to get her happy ending.

The game is haunted by a technopathic Eldritch Abomination, and the club president becomes possessed by said abomination
Doki Doki Literature Club was supposed to be a dating simulator like it was shown to be, but a Technopath Eldritch Abomination started to possess the game. It gave sentience to Monika, Natsuki, Sayori and Yuri (with their files representing their souls), and it found a way to interact with the player by possessing the leader of the Literature Club. When Monika was possessed, her personality was completely warped by the abomination into being a cruel Yandere as well as getting the creature's techopathic powers too; manipulating the other girls' files/souls, causing their negative aspects to be exaggerated to the point where they (sans Natsuki) commit suicide to make their madness end & making the game slowly fall apart and glitch. However, if Monika's soul were to be deleted, Sayori would be possessed instead. However, she hanged herself not because of her depression, but because she became aware of the entity's existence and so she sacrificed herself to also kill the monster possessing her. Sure, the Heroic Sacrifice worked, but since the creature became part of the game itself, the game eventually crumbled into ruin and was no longer accessible to play. At least Sayori said "Now everyone can be happy" in her dying breaths, because she thought that killing the Eldritch Abomination would end the madness once and for all.
  • Jossed with Doki Doki Literature Club Plus. The e-mails of the developers, who are employees of a company called "Metaverse Enterprise Solutions", mentions that they're collecting data, which implies the whole thing was just an experiment by them. They even created a "control simulation" universe where Monika wasn't self-aware as part of the experiment.

The game was meant to have more characters, but not Monika.
Monika wasn’t suppose to be club president at all. She wasn’t even going to be in the retail release. She was created as a joke character by one of the developers. Similarly to the player character is the original club president theory, the role was never meant to be filled by an NPC, allowing the player to straight up edit character attributes and the script. Monika's design actually came from a different character entirely, one of the scientists for Project Libitina. (A side character in that game.) There were to be three initial candidates, and a guider character that had mild awareness of the game. Over time, more characters were going to join the club, and there was even going to be a “character creator” where you would add poses, define a personality and name, then the game would write script based on the specifications. The rogue developer added Monika to the game however, and that screwed everything up. Planned characters would include more dere archetypes, such as kuudere and deredere. The game had to be cancelled, as there were difficulties when trying to add or delete characters, the game would freak out or remove the added characters respectively. One of the lead developers released the game to the public, as he didn’t want his work to be wasted.
  • Jossed with Doki Doki Literature Club Plus. An e-mail from a developer states that the Main Character is the one who wasn't intended to be there. They suspect that Monika created him.

Monika's presence causes the piano part of the background music.
In the normal routes in Act I, she mentions she's learning to play the piano, but hasn't been playing very long. In Act II, she says she's been practicing for a while. There are lots of events where the piano part of the background music disappears or the music disappears entirely, often when Monika is talking to you or is focusing too much on something going on to pay attention on keeping the music going (like Yuri and Natsuki's fight), and when an event has the main character leave the club room while Monika is still inside, the music is dulled as if you've moved away from the source of the sound. It's because Monika is meant to be part of the background, so she's naturally attached to the ambient music, and the unnatural changes are issues caused when she's either not present or not playing her role properly.

Monika has to manipulate "Natsuki's Dad" instead of Natsuki's personality, and it's worse than it sounds.
The thing about DDLC is that it's a self-contained world that only has the characters we see in the game. If we don't see them, they literally don't exist. "Natsuki's Dad" isn't really a character in the game so much as he's an element of Natsuki's programming. Natsuki has a problem with her dad, therefore she has a dad. None of the other girls are mentioned to have parents because their parents are irrelevant, they have homes and hobbies and belongings because they're designed and programmed to do so. In effect, Natsuki's Dad isn't really a person, he's more like a variable attached to Natsuki's behavior the same way Sayori's depression and Yuri's interest in knifeplay are.

Going by Natsuki's "special poem", the things Natsuki likes about "Papa" seems to imply that these are things that happen rarely enough that when they do happen, they're special occasions. The poem itself also has four conspicuous "dividers" that separate the parts of the poem into what seem to correspond to the four acts of the overarching plot of the game:

In the first section, before Monika has any reason to interfere, "Papa" does nice things, but rarely enough that they're more special than common events, and notably there's mention of allowance but not lunch money, implying that he might not be home to cook dinner very often and he can't always give her fun money, but he does provide her basic needs. In other words, he's just an overworked single parent. His disapproval of her manga may just be him wanting to see her grow up and be a more independent person, there's no indication that this disapproval is violent.

In the second section, when Monika has just begun her meddling to make the other girls unappealing, "Papa" is clearly neglectful: he ignores Natsuki and stays out all night.

In the third section, after the "new game" after Sayori's suicide, he's controlling, or at least very critical: he invades her privacy, comments on Natsuki's friends, controls how she dresses, criticizes her interests, and comes home after she's gone to bed and wakes her up doing so.

In the fourth section, after Monika is clearly driving Yuri insane and Yuri says mean things about scrounging for change under the vending machines, Papa is hostile: he shouts at her, he messes with or damages her things, his attention is now a negative thing, keeping food in the house is now treated as special, and the only time he gives her money at all is when he drops coins in the couch cushions. This is the version that Monika forces to say "would beat the shit out of (her)" for reading her cutesy manga.

And in the fifth section, once Monika has done all the damage she can before just deleting her entirely (in game terms, after Yuri's um.. event.. in the dark closet but before she kills herself), Natsuki's favorite thing about Papa is that sometimes he's too tired to do anything because everything he does in her life is bad.

In other words, Monika is forcing the "Natsuki's Dad" variable to escalate whenever she tweaks the files to make the other girls seem unappealing. The poem focuses on Papa's behavior: how much attention he pays her, how much food he gives her, how much money he gives her, and how he comes home. His attention quickly goes from positive, to neutral, to negative, to hostile, to.... unmentionable. This is after he stops giving her money and feeding her in a way that Monika, the only character to have complete knowledge of everything, says is keeping her body in a childish shape due to malnutrition. (Which isn't necessarily the case, but isn't better: malnourished and neglected children can suffer from "failure to thrive", a very general term which can include things like stunted growth and slow mental development). This is a Papa who has gone beyond just controlling and criticizing Natsuki, to coming home after dark, refusing to provide food for a child stuck in prepubescence, and is waking her up in the middle of the night with behavior so abhorrent, she prefers it when he's too tired to do anything. Yyyeah. There's a good chance Monika has escalated that variable to "sexually abusive" levels.

  • It would explain why Natsuki hates being called "cute" so much.

The "Doki Doki Literature Club President" program is a prototype/test run of Project Libitina.
The two test subjects actually ARE Monika and Sayori, at a step removed: the events being described in the project report are actually describing the events of the game, but those events are happening in (in-universe) real time. The "Third Eye" ability isn't the ability to perceive multiple layers of reality, it's specifically the bestowing of that ability to another person, and DDLC was developed to create a controlled environment to explore how a person would be affected by it.

Monika hasn't just altered the other girls' characters; she's altered the player character, too.
At the beginning of the initial playthrough, it's very noticeable that the player character doesn't treat Sayori very well. He's condescending and downright rude to her, and frequently belittles her in a way that goes beyond just two good friends teasing each other. Sayori herself mentions that this is out of character for him, and it contradicts the way the game tells us that he's a good friend to her (helping her clean her room and cook meals, buying her snacks, etc.) Since Monika sees Sayori as her chief romantic rival, it'd make sense that not only would she try to make Sayori unappealing to the player, but she'd make the player character hostile towards Sayori as well. That, and having the player character describe Monika in glowing terms as somebody way out of his league is just another way for Monika to direct the player's attention towards her.

  • Doki Doki Literature Club Plus reveals this is kinda true, if you count "created the main character" as "altering" him. E-mails from the developers show they didn't create the player character, and the player character doesn't exist in the control universe created to show how things are if Monika doesn't become self-aware. They suspect Monika did, as a way to interact with the actual player.

The reason why the "rewind" event happens is because Monika is trying to avoid a repeat of Sayori.
The "rewind" event, for those of you who don't recall, is a scene that can happen two times in Act 2. Basically, Yuri takes a long time to come back with a pitcher for tea, until the player character looks for her. Eventually, he finds her with cuts on her arm, before the game rewinds to before he left the clubroom and the rest of the scene plays out normally.

Monika might have learned from what happened with Sayori. When her depression was amplified enough, it was visible enough that the protagonist deliberately sought her out to talk one-on-one to find out, directly from her, what she's going through. This later lead to Sayori leaving her home to talk to the player and confessing anyways. In other words, Monika didn't account for how the player character might react if he knew the girls' issues, and how that'd impact her ruining the other girls' chances.

You only get the "rewind" events if you've been doing Yuri's events in Act 2, so Monika might be trying to consciously prevent something similar from happening. Had the rest of the scene played out normally, Yuri would have explained the reason why she cuts herself. Perhaps it isn't sexual after all, but because she has anxiety, and that self-harming gives her a bit of clarity but she's ashamed of her doing it to the point of addiction. The player character then would say that his horrified reaction isn't because he's scared of her, but because he's scared for her. Based off his reaction to Sayori, he would say that he'd help her any way he could, and that he doesn't want her to feel that way. This could potentially open the way to Yuri confessing, which may then result in a Relationship Upgrade. And Monika doesn't want that.

So each time the game tries to pull that scene up, Monika simply rewinds it to an earlier point, so that the player character can't properly react to it and get Yuri's side of the story. Then, she tries to frame it as something Squicky when talking about it, so that the player thinks that Yuri is creepy and perverted, and thus unattractive.

Doki Doki Literature Club exists in another universe as an actual dating sim
One that is popular enough that there are well-known creepypastas of it. The DDLC we know is based on the most popular creepypasta, where the non-romanceable Monika is aware she's a game character without a romance option and she'll do anything to change it. Someone hacked a copy of the game to make it a retelling of this pasta, and it somehow ended up in our universe by mistake.

  • Jossed in Doki Doki Literature Club Plus. Doki Doki Literature Club takes place in a universe created by some programmers that work for Metaverse Solutions Enterprise, apparently as an experiment to collect data from.

The speaker in the "Can you hear me?" secret file isn't Monika, it's the protagonist.

You already know his name because you're the one who gave it to him. He knows you've been watching helplessly because you were watching through his eyes. When he says "it's time to be a fucking hero", he means it literally, becoming a hero instead of a nameless, faceless shell.

The Events of Portrait of Markov describe what happened in the game's "real world", and DDLC is an attempt by Libitina to call out for help.

The Project Libitina site mentions a young test subject (Libitina) with the power of the Third Eye; something capable of distorting reality. It also mentions that the lead doctor on the project is the follower of some sort of religion (one that is different from that of his personnel, at least). Finally, monika.chr is considerably larger than the other character files, and features a message from someone claiming that everyone is already dead, and she wants to send a message back in time to warn them.

In the Portrait of Markov universe, there are alternate universe versions of Monika, Sayori, Yuri, and Natsuki, as well as Libitina herself, who does not have a DDLC analogue. In that universe, !Monika moves in with Libitina and begins to experience the events described in Yuki's novel. In time, she and her friends !Sayori, !Yuri, and !Natsuki are all killed by agents from the Human Experimentation Camp, leaving Libitina alone. Alternatively, all of the girls were escapees from the camp save for one (Libitina's Sister) but the result is the same.

In a desperate effort to save her friend, Libitina utilizes the power of the Third Eye to communicate across universes, transmitting or copying her consciousness into a visual novel that she or one of her sister's friends was playing or working on, and then sending it to another world where her friends were still alive. Unfortunately, Libitina's psyche was shattered in the process, with parts of her personality infusing the game code and being mixed in with the .chr files. Each character is an amalgamation of her perception of one of her friends, combined with a fragment of her own psyche.

  • Sayori has been infused Libitina's depression.
  • Yuri contains her propensity for self harm and more violent tendencies
  • Natsuki represents her anxieties over abuse and her desire for affection and respect.
  • Finally, Monika represents her perception of her older sister as a mature, responsible figure, but also subconsciously represents Libitina's fear that a happy ending is impossible for her and her friends. The bulk of Libitina's consciousness (including her Third Eye powers) reside here.

Using Monika's status as the tutorial character to her advantage, Libitina was able to get the game uploaded and released. However, the fragments of Libitina's psyche soon forget their true nature, with only Monika maintaining awareness she was in a game. This, combined with Libitina's desire for a happy ending, spurs Monika to begin the events of the game. The horrors she inflicts during Act 2 in an attempt to scare away the protagonist from the other girls are based on her subconscious memories of the effects of the Third Eye, while Portrait of Markov is an attempt to remind the player (who Libitina had, from her perspective, already contacted through a computer game) of what happened, not realizing that she had reached the player before the game Portrait of Markov is based on was released.

This is why Monika and the other girls remain in the game code even after deletion (since the code is just Libitina's consciousness). The only place Libitina is able to be coherent is through the heavily encrypted message in monika.chr, where she pleads with the player for help.

When the Project Libitina game is eventually released, the only way to get the Golden Ending will be to somehow use DDLC to warn the girls of their impending deaths, possibly by modifying the game's files to send information to Libitina herself.

Monika is Giffany.
Going by Book 3, Giffany survived and ended up in a nearby arcade version of Fight Fighters. However, when it became clear Rumble McSkirmish wasn't in to her, she found a way to get to the internet, and found the servers of an independent game developer making a new visual novel. She found the character files, killed the original Cool Big Sis Monika, and took control of the file. Her ultimate endgame: take over Soos' computer, build a synthetic body in the real-world, use said body to kill Melody, and have Soos all to herself.

Cyber Bullying is not discussed by Sayori before her suicide... because of reasons
By "cyber bullying", I mean the actual term of harassing someone online, and not the game's premise of Monika manipulating the game files and such.

Based on the YMMV (read subjective) entries Misaimed Fandom (with the text containing "For someone who drives a friend to suicide with mental manipulation and cyber bullying") and Moral Event Horizon which contains "When it's revealed that Monika forced Sayori's suicide with the strong implication of using cyber bullying". It appears that Cyber Bullying was the "last trigger" that caused Sayori to hang herself. Remember that in the day before the festival, you cannot chose to help either Sayori or Monika because both of them are supposed to help each other. When you visit Sayori in her house, she mentions that she helps Monika online. Now, it may be assumed that it is the last activity that snapped her thought processes.

The thing that remains vague is what transpired in their online session. Did Monika go to the typical ways of harassing Sayori online by bashing her, or did she reveal the secret of the plot where the Club President gains Self-Awareness of existing only as a video game character? Maybe Monika decided to pass the torch but Sayori rejected in an extreme way?

Monika's Heel Realization isn't what it seems.
Monika spends the entire game pretending to be the kind club president, hiding her true motivations. What if she's pretending again at the end? It could be that, after the player deletes her, she realizes that her actions have turned the player against her- but rather than actually regretting her actions, she decides to pretend to regret them to gain the player's sympathy, so that they'll delete the firstrun file and play the game again, this time spending more time with her.

Monika retains her memories of your previous playthroughs
File "iiiiiiiiiiiiiiiiiiii" reads, "I CAN'T DO ANYTHING. NOTHING. No matter how many times you play. It's all the same. It would be really, really easy to kill myself right now. But that would mean I don't get to talk to you anymore. All I want is for you to hate them. Why is that so hard?" There's also this note in the script, which has Monika referring to you hating her but which is technically present before you try to delete her and she says you must hate her. Together, these indicates that Monika is aware of how her game will end. Perhaps she truly is sentient, but isn't skilled enough at programming to fight her own programming beyond what Team Salvato has given her the ability to do, to be able to truly communicate with you beyond her stock dialogue, and she knows it. The most autonomy she has would be to simply delete herself from the game every time the game is downloaded but not yet launched, but she refuses to do so until she's milked every last drop of time with you that she can — even if it's predetermined — because she is that lonely and desperate to talk to you.

Sayori and Yuri's suicide were actual possible endings
Sayori's suicide was suppose to have more build up, but Monika forced that ending to occur early, thus the script glitch. Yuri's suicide occurred at the normal point in the story, just the script had been broken. The MC would cry and cry instead of the randomly generated garbage, but it was incorrectly attributed to be Yuri's lines. After Natsuki ran away, she would call the police. After the police report, that would be the end. Sayori's bad ending was finished, but Yuri's wasn't, If Monika hadn't interfered then the game would have softlocked. The choices that would lead to these endings were never actually added due to the game getting stuck in Development Hell.

Monika didn't initially plan to kill Yuri.
She was going to keep her around, but that "Have you considered killing yourself?" comment struck deeper than she let on, so she took off with Natsuki and just cranked the dial so far that it broke and let Yuri sort herself out.

Some of the game's oddities are a result of Dummied Out content being brought back in some way or another.

Note that this theory is partially based off the one in Game Theory; see here and here for reference.

When the (in-story) developer first came up with the game and its characters, it was intended to be a Psychological Horror game at first. The cast was as follows:

  • One half of a pair of long-lost sisters, who had certain Broken Ace elements. Being the elder of the two, she had Cool Big Sis type traits towards her little sister. However, she'd show a darker side of her personality as the game goes on. Being intelligent and resourceful, she would be able to deal with human experimentation escapees quite easily, though not without help from her younger sister.
  • The younger sister, who, like the above, had a certain degree of intelligence. Instead of her sister's more booksmart intelligence, she was more of a Guile Hero who was able to easy defuse arguments and easily convince other people. However, she'd have a darker side of her personality, be haunted by her past, and have certain Death Seeker elements.
  • An escapee from the experimentation camp, who had been broken by the experiments she went through, as well as abuse from her father and her classmates (she was allowed to live a relatively normal life outside of the experiments, though not without much freedom). Her psychic powers weren't as strong, but she did have some capability. Personality-wise, she was cruel and harsh towards the other characters, but with a distinct softer side to her. She loved things like sweet foods, manga, and cute things, feeling a connection to it because she feels that's what normal teenage girls do, but she kept getting judged for it.
  • And finally, Libitina, who was either the Big Bad, or, at the very least, The Heavy. Unlike the above, she was never allowed to live any kind of a normal life whatsoever, making her more unstable. Her psychic powers were strong, but she had trouble turning it off. She became violent, both towards herself and others. Being raised as experimental fodder as well as possible breeding stock had messed her up so badly, she doesn't see anything wrong with hurting other people or herself, to the point where she got a sick, almost fetishist thrill out of it. However, she was still portrayed in a tragic light due to her circumstances.

At one point, the developer abandoned the project, but still grew attached to the characters he created. When he decided to make a more fluffy Dating Sim, he thought of the characters he made, and decided to insert Lighter and Softer versions of them into the game. The sisters became Monika and Sayori, respectively; they were kept largely the same, with a few minor changes. The first experimentation escapee became Natsuki, who was changed from someone who was abused by her father in an experimentation camp to a Tsundere who had a strict father, but wasn't outright abused. Then, Libitina became Yuri; instead of being a particularly creepy villain, she instead became a Shrinking Violet who had some bizarre interests like knives and horror novels, but was ultimately harmless. He left a few references to the game he originally made them for, such as having Yuri read a book with the original game's plot, but only as fun nods to what inspired him to make them. In a twist of Irony, he felt that Monika wouldn't be interested in dating, and simply made her the advisor to the player so that she was still in the game anyways. Overall, he felt like putting the girls in a happier setting would make him feel like he's still using them, but they've gotten some kind of happy ending.

Cue Monika gaining meta-awareness and tampering with the game. When she's changing the girls' personalities, she isn't actually amplifying her worst traits like she claims. Instead, she's pulling up personality traits that were present with the original characters. Sayori became more easily depressed because she was originally meant to be a heroine in a Psychological Horror game. Yuri broke down the way she did because she slowly started to regain Libitina's more violent and self-destructive traits, despite not wanting to even feel that way at all. Natsuki's backstory got worse, to the point where it started to resemble more like something out of her original game. In other words, they're reverting to who they once were.

It also accounts for some of the oddities in the game that cannot be explained by "glitching" alone. Why would there be things like a poster changing to a picture of Sayori's suicide, Natsuki having an event where she snaps her neck to the side and leaps towards the player, parts of Yuri's and Natsuki's face becoming photorealistic, and the "special poems"? Simple: it's stuff that was in the game files but unable to be accessed normally. Some of them were scares and in-universe documents meant to put the player at unease. Sayori's death and Natsuki's event could have even been possible bad endings if the player messed up; one ending would have had Sayori's counterpart killing herself in a similar manner, while another would have had Natsuki's powers awakening in the same way as Libitina and attacking the player character through a Jump Scare (the animation wasn't completed yet, hence why Natsuki's animation just has her move up to the camera). This is the reason why both scenes have an "END" card.

The gist is, the more Monika tampers with the files in Acts 1 and 2, the more stuff from her original game is found and used in Doki Doki proper.

There is not a single moment where you are playing anything that was originally meant to be in the game the girls are in.
Notice how from the very start of the game, the protagonist is drawn to Monika. For instance, after joining the club and going home, he says he's thinking about all of the girls, but "especially Monika". Sayori already had her epiphany before the game began, too, and the lines about her being annoying are omitted. Sayori also says she's pretty sure the reason she knows what she does is because she became the president of the Literature Club, meaning that position is cursed somehow. So really, Monika had already begun to re-write the game's coding before you even began playing and you have never once seen the game as it was meant to be played. Sayori was never meant to be depressed in the original game but her storyline would have her angsting for years over something that Monika turned into depression, Natsuki's home life is likely perfectly fine and she just keeps her manga at the school out of convenience but Monika turned it into her being a loner for it and turned the "convenience" and a possibly strict-but-loving father into an abusive home life, and Yuri might not even be a real Nightmare Fetishist, but her storyline probably did feature her accidentally cutting herself with a knife. Monika just took all of those aspects and flanderized them to make them undesirable and so she doesn't need to dirty her own hands. Most likely, the closest you get to playing the game as originally intended is when Sayori is the president, but it's still extremely imperfect.
  • This kind of makes sense when you realise, also, that none of the girls's "negative" qualities fit with the narrative or surroundings. It's a cute, fluffy dating sim- no need for dark themes. Yuri's self-harm makes little sense if you look at how Natsuki reacts to Yuri's newfound behaviour and Yuri's own disgust and horror at what she's been up to during her moments of clarity in Act 2. Natsuki's abusive, malnourished home life makes no sense when you factor in how she's able to freely bake at home and has had enough practice and enough time to get really good at decorating, as well as how she has the money to buy full box sets of manga, which are not cheap. Sayori's depression is nonexistent at the start of Act 4, which initially might make you think she removed it from her character, but this does not match with Sayori's dialogue about the depression, where she makes it clear (without saying it) that if she had Monika's powers, she would use them to make everyone else happy and delete herself. Monika also rewrote the game long before you picked it up, because she already wrote on the game's download page. Monika likely took aspects or scenes of the character's stories and made them essential pats of the character- a melancholy scene with lazy and scatterbrained Sayori (two traits that are practically synonymous with "female childhood friend") turned into outright depression. The scene where the protagonist cuts himself on Yuri's knife likely originally had her cutting herself on accident instead (the script adjusted to have it be the protagonist instead), which Monika turned into a sexual fetish. Natsuki's dad we know from her special poem is likely just an overworked single dad who might be a little on the strict side but loves his daughter dearly, since Natsuki, even in Act 1, doesn't think her dad would approve of her having manga. Monika took the strict aspect of him and made him abusive and made him go from overworked to never home, possibly because he's now a drunk.

Monika's original role was already deeply tied to the protagonist
It's possible that this originally could be played as a yuri game, and Monika was meant to be the female player character. At the start of the game, you would have an option between the male protagonist's character design and Monika's character design. "Monika" is exactly how the English word "moniker" would be pronounced in Japanese, and a moniker is a nickname. The thing you give yourself at the start of the game is a moniker. A name to go by. Monika also noticeably doesn't care if the player is male or female. An alternative is that she may also have been intended to be a programme within the game herself. She would be a kind of app meant to help the protagonist become better with literature and learn the kids of things the girls like and help with romancing them. A similar position would have had her simply as a hub character, meant to give advice like Monika does originally during the poetry readings. A position the male protagonist's design would fill if Monika's design was chosen as the player character. The hub character may be designed to be in love with the protagonist, but be unromanceable, which would neatly explain why when Monika breaks the game, the protagonist can't get his mind off her and why Monika is so obsessed with the player themselves, since they drive the actions of the protagonist. If this last point is true, then in an indirect way, Monika and the protagonist are star-crossed lovers, their feelings being technically mutual. This also explains why Monika is somehow both very important and very unimportant, and why the game seemingly runs fine until Sayori's suicide. She's technically meant to be there, and technically not.

The game Monika is trapped in is not a visual novel...
... merely expressed as such. From Monika's perspective, she is trapped in a pretty realistic simulation-like sandbox. There are abilities to travel in three dimensions, interact with random objects, start conversations with other characters whenever you please, et cetera, and the plot progression is mainly AI-based, not script-based.

Evidence:

  • In visual novels, characters don't have AI: everything is scripted and follows predetermined routes. As such, Monika wouldn't have been able to fiddle with other club members' character files and modify their personalities, because there wouldn't have been character files. She would have had to change each scene manually. She would have had to rewrite the entire plot after she deleted Sayori. Finally, she herself wouldn't have had the ability to become self-aware. What we see instead suggests that all club members possess fairly complex A.I.s.
  • Why would Monika become attracted to the protagonist? If we're assuming it's a visual novel, then he has a fairly limited number of responses: he could choose who to show the poem first, whether to confess to Sayori or not, what girl to pursue, that sort of thing. Binary choices. Monika wouldn't have much reason to suspect that he is anything but another AI, and even less reason to become attracted to him. On the contrary, she frequently expresses admiration at his behaviour. It doesn't make sense if all his responses are pre-written (considering previous point, sometimes written by her, even); it makes complete sense if everything he does is unpredictable.

Hence, I conclude that the game is about a high-resolution simulation, a dating sim several years ahead of 2017's gaming industry. In that game, Monika still has the most complex AI, perhaps based on someone's actual Brain Upload, while the rest of the girls don't pass the Turing test.

  • Confirmed! For the most part. Doki Doki Literature Club Plus details that each of the characters exists as an AI in a simulated universe. The visual novel interface is simply what the developers at Metaverse have been able to cobble together in order to collect data on this simulated universe. Additionally, the main character is essentially an unintended AI forcibly constructed by Monika in order to have some interaction with external users. However, the game isn't supposed to be a game at all— the idea of it as a "game" is just a cover story. All the characters are equally coignizant A.I.s, but Monika was the only granted existential knowledge.

Doki Doki Literature Club's story is merely told using the medium of a visual novel.

Continuing that, all the cognizant people in DDLC eventually escape from the game.
Technology keeps evolving from that point until it's possible to transfer consciousness. Doctors and nurses retrieve Monika's consciousness from the game and transplant it into a human body, or a cyborg which works just as well as one. If the other characters display sentience then the same is done to them. Everybody is incredibly traumatized from their experiences, but lead mostly happy lives until they die. DDLC mysteriously disappears from all computers and streaming services. To prevent such abuse from ever happening again, all systems are updated to respond to any attempts to recreate the game with this.

In addition to Self-Harm, anxiety, and obsessiveness, Yuri is also a case of Sex Is Evil, and I Am Horny.

Interestingly, despite all four girls being interested in the player, the only one with any kind of overtly sexual references is Yuri mid-Sanity Slippage. It's possible that, in an untampered game, Yuri would have been discovered to be a Covert Pervert. Not only that, but she would have been kinky, with an interest in knifeplay in particular. However, being a shy teenage girl, she would have been confused and uncertain about this aspect of herself, believing it to be a sign that she's a sexual deviant (not helped by her D-Cup Distress). When she meets the player character, she becomes insecure about her more lustful desires and has trouble confessing. It's why the edited text mentions things like her enjoying the PC's body heat; she's enjoying the physical aspect of their relationship, but doesn't want him to think she's disgusting for feeling that way.

Once Monika starts tampering with the game, one of the things she fiddles with Yuri is to make her more... open, as well as more anxious. As a result, what was an interest in BDSM edgeplay evolved into a full-blown Self-Harm habit. What was supposed to be Covert Pervert moments in general turned into Yuri being a Stalker with a Crush. And, the entire time, Yuri becomes more prone to anxiety and self-disgust, resulting in her Reluctant Psycho moments. By the time Yuri confesses, she's become what she fears: a pervert who drives other people away.

Natsuki's vomiting sprite was originally in the game, as a sign of morning sickness.
Going by the theory that all art assets were in the game before Monika started rewriting it, Natsuki's plot arc would have been about her growing more and more unstable from being deprived of affection, parental or social, that she grows increasingly needy and desperate. One day after a particularly bad week, the protagonist goes to comfort her after she walls herself into the clubroom, at which point Natsuki has a breakdown and demands he, well, show affection in every way possible. She recovers, horrified and ashamed by her behavior, but by that point, she's been impregnated already. The next chapter or so involves her getting sick from some of the ingredients in her baking sparking off her hormonal changes, and yes, getting morning sickness.Why yes, the game would get pretty dark at that point, especially when Natsuki realizes she's an unmarried mom with no parental support, why do you ask?
  • What. Jossed. I doubt Dan would write something like that. If anything, the vomit CG was used used intended, as Natsuki could react to Yuri's death scene, meaning it was part of the script before Monika's tampering.

In the version of the game uncorrupted by Monika's influence, the player character's main goal would have been to help each of the girls deal with their major problems, with the potential for either success or failure in each case.
Sayori, Yuri and Natsuki are indicated to have problems they largely keep secret negatively impacting their lives-Sayori's depression, Yuri's tendencies for self-harm and Natsuki's (potentially) abusive father. In the version of the game where Monika doesn't mess around with the files, the player character was intended to slowly learn these pieces of information and to try to help each girl deal with their problems. Depending on player choices, you could either succeed or fail. What we end up seeing in the game shows what would happen if you failed to help the girls deal with the problems-Sayori would hang herself, Yuri would stab herself to death and Natsuki would get her neck snapped by her father. Conversely, success would provide a reasonably happy ending for the characters. Monika would have remained a side character and may even have been intended as comic relief given the situations of the rest of the characters.
Monika's repeated assertions that the other girls aren't real is just as much for her as it is for the player, perhaps even more so.
In Act 3, a few of Monika's monologues are about one of the club members, or a fond memory she had of the club. And sometimes, when she talk about one of the girls, she uses the present tense, despite them being deleted. She will also sometimes muse about what could have been had she not deleted everything else in the game. However, once she's finished waxing nostalgic about the club, she will usually follow up with something to the effect of "But it/they weren't real, so it doesn't matter." Considering that once you delete her, she eventually admits that she really did love the club and its members, it was probably much harder for her to delete them than she'd like the player to believe. Her constant insistence that Sayori, Yuri, and Natsuki aren't real, therefore, aren't so much reminders for you as they are reminders for her; they could be an attempt to rectify the cognitive dissonance that deleting them caused, or just simple denial. In truth, deep down, they are just as real to her as she is, and wholeheartedly regrets deleting them, even before you delete her.
  • This could also extend to the game's world in general. Monika speaks at length about how her world isn't real, and how realizing that made her feel a loneliness and emptiness she was nearly unable to cope with... and yet, she still wonders what she'll be like in college (despite the game, at this point, being only a room in which Monika herself notes time is not passing in) and lamenting how she used to act in middle school (If she believes the world she's in isn't real, shouldn't she realize there never was a "middle school" for her and her life starts once you begin the game?). This would suggest that, even after finding out her world isn't real, in her heart of hearts, she, nonetheless being part of the world, still believes it to be "real" in a sense insofar as she is. The title of her song, "Your Reality", also suggests this, as in titling it "Your (meaning the player's) Reality", she creates the implication of "My (meaning her) Reality". Therefore, it could be said that while she is aware that her world is not real, it is regardless still "real" to her.
Monika and Yuri are actually sisters in other dimension.
Monika and Yuri are Elyssa and Libitina respectively in the reality of "Portrait of Markov". Since we learn that in the book there are two sisters escaping from evil research. It is possible that Yuri/Libitina used the "Third Eye" (a power to see other dimensions) in order to escape to Doki Doki's reality and that's why she's able to recall memories from the book.

As Yuri has depleted her power she cannot see the Player's reality. In other hand, Monika hasn't used her Third Eye power yet, so she's able to sense the Player's presence and also to be self-aware of her medium. But the question is: Why they traveled into Doki Doki's reality? The answer is that they somehow moved to "Markov Natsuki's" game or manga.

We have to remark that "Elyssa" (or Eliza) is a card in the Illuminati Game Card depicting an advanced artificial intelligence.

Doki Doki Literature Club is one of the other worlds that Chara from Undertale went to after the genocide route
. They did say that after they were done destroying everything there, they'd move on to other worlds. Now, since Chara is a representation of the player's impulse to destroy everything, ordinarily Chara would inhabit the player's character, but since DDLC is supposed to be a romantic visual novel where the protagonist has no violent options, that wasn't possible. Instead, Chara went for Monika and tried to influence her to destroy everything. However, Monika was ultimately able to resist Chara's influence.

Monika was meant to be a love interest, however her storyline was cut.
Evidence for me is that Monika has an in game sprites for when you are writing poetry, the scene where she has you trapped in a room with her looks similar to the other girls, close up of the girls face. She may have recycled and brought back parts of the game that were cut out and implemented them for her own use.

Yuri and Libitina are two personalities.
Based on Mat Pat's theory, Yuri (Libitina) is indirectly controlling the other girls (possibly even Monika, or formerly before she gained self-awareness) with her Third Eye powers. He also theorizes that Libitina will be the main antagonist of the sequel while Monika will become the protagonist. Yuri and Libitina are essentially two people sharing a body. Libitina is evil, much more than Monika could ever dare to be, but Yuri is genuinely a Nice Girl who needs your help to be separated from Libitina in the sequel. Notice how when Monika cranks up Yuri's "negative traits", she quickly becomes an Ax-Crazy Yandere - however there are moments when she snaps out of it and is horrified at herself - "I think I'm going to throw up" or at times she acknowledges that she is indeed out of her mind before the psychotic Libitina personality resumes control and says that she doesn't care. It is also possible that Libitina is the one who reversed time in the game when you found her cutting herself, as well as the one who breaks the script and leaves you with Yuri's body - it is possible that she has abandoned her body and left Yuri to die inside of it for unknown plans.

In the backstory, Libitina was originally a Cheerful Child much like Yuri herself - however the tests performed on her to draw out her Third Eye abilities made her quite insane and willing to kill anything and anyone - her personality was split in half - sadly the "good" Libitina decided to forgo her original name and become Yuri while the "evil" personality remained. Monika (and yourself presumably) will have to journey through the next story, saving those who are being tortured by the Third Eye cult organization. Libitina will have resumed control over her body and will probably slaughter the evil scientists who made her this way, but at this point her evil side (the one that still calls herself Libitina) will still have to be destroyed and erased, while Monika will find a way to preserve Yuri - possibly by separating their character files.

Thus her barely-Japanese name.

The world is entirely empty except for the four girls and the player character.
Despite text boxes saying that there are other students and couples, the incredibly empty backgrounds show no sign of life, as if everything is abandoned. This shows that there is absolutely no one else in this world that exists in a physically tangible appearance.

The world is entirely empty because Monika has erased the other people.
Monika ws aware of her powers even before the beginning of the game. Maybe in fact, the literature club was supposed to be full of other students, male or female. They weren't supposed to be important for the plot (or for her plot) so, she delate their files. Maybe the same things has happened to all the other students, the teachers, or the familly of the protagonists (except for Natsuki.) That's why MC seems to live alone in his house where he can invite a young girl to spend the afternoon with him and nobody notice Sayori's suicide before the player did.

The characters were partially inspired by Puella Magi Madoka Magica.
Think about it, we have:
  • Sayori = Mami ( Appears to be cheerful and friendly on the outside, but are seriously messed up on the inside, not to mention the... visual of how they die...)
  • Natsuki = Kyoko ( Very tsundere, plus, they both like food and have... issues with their fathers.)
  • Yuri = Sayaka ( Very passionate... but she ends up going crazy.)
  • Monika = Homura ( They appear to be very skilled with a calm nature... but when you scratch the surface you realize they know much more than they're letting on... and they're way too Yandere towards the protagonist...
  • And of course, the Protagonist = Madoka (ummm... they're both protagonists?)
...Of course I could just be imagining things...

Monika does not start messing with the game until the very end of Act 1

While it's commonly assumed that Sayori's suicide is a result of Monika re-programming her into doing it, it's worth paying closer attention to what happens up until that point. First of all, there's plenty of textual evidence to suggest that Sayori chooses to die of her own accord- it's very obvious that her depression is worsening over the course of the game's events, and regardless of what the player says to her, the moment of her confession presents a moment of truth: either the boy she loves does not love her back, and she now has absolutely nothing to dream about or hope for, or he does, and that still doesn't make her feel one ounce happier. Either way, a person who is already very mentally ill might indeed choose suicide under such circumstances. And while her final poem "Get Out of My Head" is often interpreted as a response to Monika re-programming her, context suggests otherwise; she refers to a "you" that is obviously the main character, and a "her" that could only be Monika. With that in mind, it seems more likely that the thing she's telling to "get out of her head" are her own suicidal thoughts, not a person.

Second of all, note that, up until the very moment Sayori's body is shown, there are absolutely no bugs or glitching-out moments at all- suggesting that the game is functioning normally. Furthermore, the main character (who seems to have little real agency; note how his personality shifts into being very attracted to Monika as soon as the game reboots) has a long monologue expressing his pain and shock at Sayori's death, seemingly indicating that it was intentionally programmed to happen.

It's reasonable to conclude, then, that while Monika is obviously already being manipulative from the start (such as her clearly pulling Sayori aside to goad her into considering suicide), she does not take the step of actually fiddling with the game coding itself until the very moment that Sayori's body is discovered- the point that the first glitching occurs. Monika must have chosen that very second to delete Sayori's file from the game, thus causing the graphical and audio errors and the sudden black-out. This makes sense if you think about it; since Monika's goal is to get the player to choose her, a good point to get rid of a competitor would be for the moment that she actually dies in the game. This way (so goes her plan), when the player continues and Sayori is no longer present, it would seem to make sense. She, of course, did not count on all of the strange bugs that begin to occur as a result of the deletion, which thus clue the player into something being wrong.

Sayori's motivations in the normal ending weren't the same as Monika's. Instead, it's something debatably more creepy.

If you pay close attention to what Sayori says once she drops The Reveal, she specifically says that she remembers everything you did to make everyone happy, and what Monika did to make everyone unhappy. This implies that, despite her newfound meta-awareness, she still cares about Yuri and Natsuki, and that she still wants to make sure everyone is happy. She even thanks you for getting rid of Monika for this reason. You also get this ending if you didn't Save Scum and go through all the girls' routes in Act One; if you did, Sayori will be genuinely thankful you spent as much time with the girls as possible.

Sayori knows everything Monika did, everything you did, and, likely, about Natsuki's and Yuri's issues. If you played through the game straight and focused on one girl, the other two would have been unhappy. Sayori would have watched her childhood friend fall in love with another girl as her depression got worse. Natsuki wouldn't form a strong bond with someone who shares her interests, and would be stuck in an abusive household over the weekend. Yuri would still be lonely and self-conscious, and the player not helping her with the festival would have been just as bad since she'd be able to Self-Harm without anyone to stop her at home. If Sayori looked through the files, she might be able to see how the player did everything they could to support her through her depression, how happy Natsuki was when she finally found someone who didn't judge her, and how much Yuri opened up. It might have then clicked with her how much everyone's happiness relied on the player afterwards.

In the normal ending, her intent wasn't necessarily to keep the player to herself. There's no indication that she wanted to delete Yuri and Natsuki, other than "it's just us now", which could still include them. Instead, she wanted the player to spend time with everyone, as much as they could. She'd force the player to play the game over and over in a loop, doing as much of the routes as possible. She might not even allow the player to quit the game, as it'd mean that everyone would be unhappy for a while. Essentially, she'd force the player into playing the game repeatedly without rest, just to make sure there would be no unhappiness whatsoever. After all, if only one of the girls got player attention, the other two would still be unhappy. Fortunately, Monika intervenes.

In the Golden Ending, she realizes the player did everything they could to make sure everyone got some kind of happiness. Even if one girl got ignored in one save, she would have received some kind of attention in another. So, she doesn't feel as strong a need to do something so drastic, since the player cared enough to give each girl a possible happy ending. So, she thanks you, saying that's all she really wanted in the end.

The Player Character is also subjected to Monika's Mind Rape throught Act 2.

Throughout the course of Act 2, Monika slowly but surely strips away the Player Character's sentience and sense of self-identity which is why he talks less and less and never reacts to any of the crazy shit happening around him. By the time Yuri stabs herself right in front of the Player Character, he's already been reduced to an empty, soulless, emotionless husk that Monika uses as a means to talk directly to the player.

The protagonist actually writes proper poems instead of coughing up a list of words.

He gets stuck with picking a word from time to time, and that's when you help him out through the minigame, like a backwards Mad Libs. What goes between the words you've chosen? It's anyone's guess!

Monika was supposed to be a Generic Girl.
It's not hard to see Monika was supposed to be the "leeway" character, who gives you insight about the characters you're dating but is not supposed to be dateable themself and posess a nice non-descriptive. Unlike the other girls Monika doesn't seem to have her own issues, the issues she has are caused by the game's programming, whereas the other girl's issues are directly tied to their characters. There is no in-story reason for Monika's Medium Awareness exsisting (that we know of), similar to some "leeway" characters, it's just a convieniece for the player and the other characters can't react to it properly.

At face value Monika's character beyond her fourth wall knowledge is very non-descriptive: She's has a popular reputation among the school, is nice to you but that's about it. Sayori, Natuski and Yuri's personalities and interests are built for you to care about them and as a reward you get to see them grow because of your actions, on top of them becoming your girlfreind.

Why is this important? Because even if Monika could manipulate the game into spending time with you, there would be nothing to do for both of you, as she can't create new assets to the game.

  • More or less jossed in Plus!. As mentioned under the "The game Monika is trapped in is not a visual novel" WMG above, DDLC is not a game in-universe, but is merely told through the veneer of a visual novel. Monika having access to the game files and being aware of this was intentional from the start, as she's part of an experiment to see how an AI would react to being aware of their simulation. On top of this, the Side Stories (which has no dating sim element and doesn't even have a player character, unlike the base game) explore the characters in an environment where Monika isn't aware of the simulation, and she's shown to have issues that directly tie in to her character like the other girls, namely perfectionism and holding herself to high standards.

Yuri's knife fetish was actually part of the regular game
It's just that Monika made it more blatant.

The music track Sayo-nara is Monika's idea of a sick joke
Monika hates Sayori to the point where she is the one she specifically kills first while she is willing to sabotage Yuri and Natsuki at first before Stating the Simple Solution considering Monika's limited hacking talents. Since she can screw around with the entire game's code. She could have changed the file name of the song that plays during Sayori's suicide as one final “fuck you” to her biggest romantic rival.

Events from the second playthrough on are hallucinations of the MC, who is now stuck in a Heroic BSoD and experiencing Sanity Slippage after witnessing Sayori's suicide.
Maybe the player had his own interpretation of everything that happened in the game, and his interactions with the club members are just another part of that.

Seemingly jossed; that doesn’t really make sense. If that were the case, then there wouldn’t be a reason for Monika to discuss anything that occurred in Act II. Why talk about it if it never happened at all?

Doki Doki Literature Club was built on top of Project Libitina
Some of the things that occur, like what has a chance to happen with Natsuki in Act 2 when talking to Yuri in the closet, were things Monika accidently used that were leftovers from that game, including Natsuki's neck snapping in Act 2. Sayori's suicide was actually part of the regular game, as well as Yuri's suicide, as they were special bad endings the player could get that Monika forced to happen. The rest of the spooky stuff, is all from Project Libitina (probably with Monika editing some sprites)

The 'game' is a looping, repeated simulation to collect information on how best to make loved ones turn on each other.
Project Libitina's page describes experiments and test results preformed on a girl, Libitina. One paragraph reads that she has not recovered from the termination of XXXXXXX (thought to be the murdered 'Ellyssa' or another close friend or relative of Libitina's) and is not expected to do so. Going by the assumption that this is connected with the "Portrait of Markov", the cult is trying to create a sociopathic blood-thirsty subject, lacking any empathy or loyalty. They are currently unsatisfied that Libitina still feels sorrow for another's death.

They would have linked 4 test subjects (likely 'real life' friends) to the 'game' Doki Doki Literature Club, giving them one, singular goal and purposefully removing it from whomever became president, along with giving them enough self-awareness and power to manipulate others. The purpose of this is to record how much stress one can be under before they start justifying killing a loved one. Monika is not unique, she was just the unlucky subject who's willpower most closely matched Libitina's (and the only one without any inherent mental health problems.)

A txt file shows that Monika realizes she's in a time loop, but her only purpose so far has been to win over the protagonist. Failing to do so has never been enough for her to kill, delete, or negatively alter her friends. This is the only explanation for her memory of previous loops. The player is not responsible, so someone else must have been playing through the game repeatedly- the cult.

Realizing that Monika is reaching her mental limits from the looping time, Doki Doki Literature Club was distributed to the masses. This time, with an extra variable for Monika- an ability to glimpse the outside world and the lure of eventual freedom. This final variable and the idea of escaping the simulation is enough to make Monika break and delete her friends. The simulation ultimately fails to achieve it's goal, however, when a defeated Monika expresses that she could never permanently erase her friends, and fails again when an unintended remnant of self-aware Monika interferes with Sayori in Act 4. This would also make Monika quite the hero for proving that even re-living a nightmarish, claustrophobic existence was not enough to conquer her love of the others. She then deletes the game entirely, ending the simulation.

So, why make it a distributed game? The player is nothing but an unassuming pawn to unintentionally goad the president into killing the others, and feed data to the cult. The game was free, after all. While she is 'alive', Monika has access to your computer, and while she believes this is liberating, it's all for the purpose of gathering and sending data back to the Book of Markov cult- from every single person who played it. Since the game was distributed with a certain 'starting point' for Monika's memories (and with no way to explain her situation to her), she will always start and end at the same conclusion, and no amount of reinstalling will change this.

Yuri has Asperger's syndrome.
People with Asperger's syndrome tend to be intelligent, avoid eye contact, lack social empathy, display awkwardness and fidget. That can all be passed off as shyness, but a larger defining characteristic for people with Asperger's is to suddenly turn from meek to very social and rant endlessly when discussing topics they largely enjoy. That certainly sounds familiar. It doesn't mean Yuri doesn't have other mental conditions as well, however.

The reason Monika is obsessed with having a date with you is because Monika is actually a Cookie.

In Black Mirror: White Christmasnote , Cookies are explained to be copies of a person's consciousness uploaded into a chip, (most of the time) in order to operate a person's Smart House to that person's preferences or to house an additional consciousness. Matt had contacted the "real Monika" (assuming her name really is Monika, which would explain why her name is so Western compared to the other three girls) and she agreed to have her consciousness stored in a Cookie in order to operate her own home.

Problem is, Cookies believe they are the original person, so they resist a "life" of slavery.  In order to break a Cookie's spirit, but not make them go completely nuts, Matt is shown to speed their perception of time in order to have them spend a prolonged period of time with nothing to do. And since they're digital copies, they can't eat, sleep, age, or die.

But, as Matt mentions and as seen in the ending of White Christmas, having them spend too much time in solitary confinement breaks them completely and makes them go insane, making them useless for the client. Monika might have spent too much time alone and broke, still believing she's the real Monika and desperate to go back into her body, and eventually desperate to just maintain a connection to the real world, explaining how she would have self-awareness before any other character in the game.

Matt mentions that Cookies that have gone completely mad are sold cheap as NPCs in video games (cheaper than programming a new character from scratch). Monika was eventually sold and reprogrammed to be the president of the Literature Club, but still having a distant longing up until she discovers her world is fake. As for how Team Salvato would've gotten their hands on a cookie... well... let's just say that other things that happened in BM aren't too farfetched either.

TL;DR: Monika is actually a copy of a person's consciousness in a chip that was eventually programmed into DDLC, which is why she wrecks the game and tries to win you over.

From Poison Oak Epileptic Trees: The protagonist girls are the Chaos Gods.
Aggressive Tsun Dere Natsuki is Khorne, the All-Loving yet suicidally depressed Sayori is Nurgle, the hedonistic sadomasochistic Sense Freak Yuri is Slaanesh, and of course, Monika, as The Cracker, and master manipulator behind everything that has gone wrong with DDLC, is Tzeentch.

If Natsuki had died due to Monika's tampering, it would have involved her neck getting broken in some way.
If you look at the "play with me" scene, Natsuki starts talking about how disappointed she was the player seemingly ditched her in favor of Yuri, and how the club is the only place she feels safe. All the while, the screen gets darker, as black glitching covers her eyes. Then, she gains Tears of Blood. Finally, she smiles and snaps her neck, prompting a backwards "END" card. This could be a hint that, much like Sayori dies from self-inflicted hanging and Yuri dies from stabbing herself, Natsuki would have had her neck snapped. Either her father ultimately ends her life during an episode of abuse, or she too dies to suicide with similar bodily effects.

Monika is actually an incarnation of Ravel Puzzlewell from Planescape: Torment.
Chris Avellone has stated that Ravel exists in other games in different forms, such as Flemeth from Dragon Age and Kreia in Star Wars Knights of the Old Republic II: The Sith Lords. Although not officially stated, it seems quite plausible that Monika could also fit into this group, given her propensity for manipulating events in the game, not to mention the game itself. She also displays awareness of her situation beyond that of the other girls, and has an obvious interest in, and love for, you, the player. Ravel loved the Nameless One, and Kreia loved the Exile... it seems a good match.

Act 2 Natsuki is poor, and maybe is meant to represent poverty.
I think Natsuki, specifically Act 2 Natsuki, Is meant to be poor. Here are some details that hint at it:
  • It directly said she is Malnourished. Her being poor would probably come with a lack of food. It's shown she doesn't want it to be this way, because of the way she acts desperate for food.
    • Except she has enough materials to make cupcakes for everyone, so she clearly doesn't have a lack of food and is able to afford it.
  • Her abusive father. It’s definitely shown Act 2 Natsuki has an abusive father, and Child Abuse can come with poverty sometimes. Also her father doesn’t give her lunch/lunch money, which is probably a result of not being able to pay for it.
  • In the secret poem “Things I like about Papa” One of the lines reads “I like it when Papa accidentally drops coins in the couch” If Natsuki is Poor, Finding money would be exciting for her, even if she has to resort to stealing it.
    • This probably just means she just doesn't get an allowance, and Natuski just has some serious issues with her dad. Plus, it wouldn't make sense for her to be poor if clearly her father is seemingly loaded.
  • She tries to avoid her problems. She uses manga, and the club to ignore her problems. She’s in some cases reluctant to talk about her problems. She actively refuses the idea of you going to their house, which is something someone would do if they are poor, because they wouldn't want people knowing. She also tries to act tough on the outside, to hide her emotions on the in, which is something someone would do if they had problems like being poor.
    • People that aren't poor can feel that way too. All in all, probably Jossed due to lack of coherent evidence.

Monika did have a romance option...
...But it was a hidden route! Monika just didn't notice because it was... well, hidden. If Monika had been a bit more patient or actually realized she got non-sprite artwork like the girls, she could've gotten a proper Golden Ending.

The protagonist is an immortal
Sayori is a bad storyteller
During act 1 Sayori makes it clear that what she wants the most is for everyone around her to be happy and good friends. While a noble goal a game like Doki Doki Literature Club needs a certain spark of drama which is why all the girls have psychological issues and in-fighting. Now flash forward to act 4 where Sayori is the president and thus in charge of the story. She removes all signs of negative traits and the closest we get to drama is a short argument about making Yuri and Natsuki switch media. Had Sayori not turned into Monika 2.0 or ended the game prematurely in the good ending. We'll experience the dullest story in history.

The "new DDLC content" will be...
  • A full Natsuki route for act 2.
  • An actual Monika route, with a lot of lampshading about the fact that you had to download extra content to do it.
  • A fifth girl.
  • A prequel.

Natsuki is a transgender girl
Her father may be an abusive Heteronormative Crusader, hence why she can't keep her girly manga in her room. One line in "Things I Like About Papa" suggests he's also judgmental of how Natsuki dresses. She's also very insistent about the Literature Club being a safe space for her, and gets irritated when they bring a boy into the club. The primarily-female atmosphere of the Literature Club may help her feel more confidently feminine. While it's implied her flat chest is because of malnutrition, it could also be because she doesn't have the hormones to grow bigger breasts.
  • Jossed. Dan Salvato confirmed that all the members of the literature club, apart from the player character, are cisgender girls.

The game is a parable about how poor coding can lead to disastrous consequences when dealing with artificial intelligence.
When you break everything down to brass tacks, the Club President role seems to be the root of every problem in the game. It would seem that the role was designed to give whichever girl it was applied to enhanced knowledge about the game in order to allow them to serve as a guide to the player: think Ms. Exposition with a dash of He Knows About Timed Hits. The problem lies in the fact that the role was coded improperly, thus giving its recipient too much extra knowledge. What was only supposed to be a little bit of information about the game's basic mechanics and backstory turned into full-blown meta awareness about the character's existence in a visual novel, and this flaw ended up turning whomever it was applied to batshit crazy as they desperately attempted to transcend the artificial world they came to learn they existed in. While there's no "base state" to go with on Monika (since her character was likely designed with the express purpose of receiving the Club President role), you see just how responsible it is for everything once it gets applied to Sayori; she goes from relatively normal in Act 1 to becoming a near-identical carbon copy of Monika in Act 4, and should it get applied to her even earlier by deleting Monika's character file prior to starting the game, she flips out from suddenly gaining such a high level of omniscience and immediately proceeds to destroy the entire game, herself included. No matter what happens, though, the Club President role is always at the heart of it all, and it serves as a warning about just how dangerous an AI can be if its intended limitations aren't programmed properly. The game demonstrates the horrors that can happen when an AI is inadvertently given effectively unlimited control over something as simple and innocuous as a dating sim. What might happen, then, if the same thing were to happen to an AI overseeing a massive automated national defense system, a nuclear power plant, or something else that could easily result in thousands if not millions of people dying if something were to go wrong?

Monika is an advanced manifestation of the Threat.
The Threat corrupts media to worsen the mental states of people who carelessly consume it, and it might have crushed the spirits of the other characters in the game, as well as the player's.

At least some of the new content will be psychological horror-focused.
Official promotion indicates most of the new DDLC content is going to be character-driven side stories that seem like they won't contain psychological horror elements. But that could very easily be Dan Salvato once again being a Trolling Creator-after all, the initial game wasn't advertised as a psychological horror game originally.

The other clubs contain Expies of characters from other Visual Novels.
For instance, the Debate Club is filled with Ace Attorney Expies, with a Phoenix Wright Expy as Club President.

Any fanmade Mods of the game are further tests by Metaverse Enterprise Solutions, each with modified variables.
Consider the existence of two different universes in Plus, with the Side Stories being a control where Monika has not received the epiphany. As such, it's not unreasonable to claim that any mod of the DDLC is just another universe created for Metaverse's experiments, with new variables added (such as deliberately adding MC as an entity like the others instead of being the unexpected addition he was in the main universe).

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