Being a Murder Mystery with lots of twists and turns from who you know, to who you are, and what you are doing in Kanai Ward. Rain Code has a lot of little hints about its massive twists long before they are revealed.
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Chapter-Specific:
Chapter 0: Massacre on the Amaterasu Express
- Plenty towards the culprit of Chapter 0:
- Their character artwork features him keeping various kinds of animals on leashes and wearing an outfit consisting mainly of fur and leather. But would a Nature Lover who can talk to animals do such a thing? The dog is even aggressively trying to get away from Zilch. Also, the only animal not restrained by a leash is a snake...
- The only detectives who don't show off their Forte are Zilch and Melami. And while Melami never gets the chance to, unlike Zilch the conditions for her using her Forte can theoretically be met on the train ride.
- Upon meeting Yuma and hearing about his circumstances, Zilch is quick to accept him despite how suspicious he is. After all, he knows Yuma isn't the one the group should be worrying about.
- It's odd for a detective who uses animals for their work, like mice, to not bring any with them. Unless they are not who they claim to be.
- Shinigami jests that Zilch could be a Bitch in Sheep's Clothing before she's properly introduced. She's actually spot on.
- Pucci gets some mild Ship Tease with the protagonist. If you've played the Danganronpa games, that's a sign she's already doomed.
- Between Yuma spotting Zilch's corpse in the infirmary and him opening the door only to find a completely charred corpse, a few minutes pass at most—far, far too little time for the body to be burned beyond recognition. A clear sign that Zilch wasn't dead after all.
Chapter 1: The Nail Man Killings
- Yuma is told that the incinerator can only be used by the Church's clergy. Which immediately implicates the Priest standing nearby as he's the only known religious leader. He's also the one who asked the watchmaker to fix the clock and has requested that a few times before. The Priest is also shown to be very sympathetic to the culprit's methods and is convinced that Jiei Colan is the Nail Man despite the incomplete information. Something the real culprit would say.
- During the Mystery Labyrinth, the third of the locked room mysteries has no additional clues to the identity of the Nail Man, and Seth's Mystery Phantom doesn't show up to dispute any of Yuma's logic as to how it went down. Yet solving said locked room is still needed to progress in the Mystery Labyrinth. The reason is that this Locked Room Mystery wasn't actually perpetrated by the Nail Man, but rather a copycat, so of course there would be no clues to the Nail Man's identity.
- In an off-handed remark while investigating the first (chronologically last) Nail Man victim, Yuma muses about how even if the bodies weren't dead, the nails pinning them to the floor would prevent them from rising up. It turns out that actually is an incredibly likely thing to happen to Nail Man victims, especially given how they were all hidden away in Locked Rooms before anyone could take the bodies away to the Testing Ground. Indeed, for the one body whose upper torso was NOT pinned to the floor, the dripping vertical bloodstain is way too long for the short time it took the Priest to set the thread up and is bleeding far too much for a corpse, suggesting he has sat up at least once.
- Just as you're about to finger the priest as the Nail Man and he turns into a Mystery Phantom to rebuke you, Seth's Mystery Phantom shows up to help him out. Now, later chapters do have logical reasons for why a Reasoning Death Match would have more than one Mystery Phantom to deal with at a time. The three main suspects in Chapter 2 are supposedly accusing each other for the murder, and in Chapter 3 Guillaume and Dominic are partners so it makes sense that they'd try to double-team Yuma. But Seth should have no connection to the priest and his excuse for defending him (that he's a man of the cloth) is flimsy. It turns out he was receiving kickbacks from the church's charity fund, and if the priest were to be exposed as the true culprit it would lose him a lot money.
Chapter 2: A Silent Curtain Call
- The intro for Chapter 2 sees the spotlights of all five main drama club members go out; first Aiko, then the rest, one by one. By the end of the chapter, they're all dead.
- Early in Chapter 2's Mystery Labyrinth, the victim herself somehow becomes a Mystery Phantom trying to explain that she committed suicide. But if the purpose of the Mystery Phantoms is to mislead people into ignoring the truth, why would the victim of all people want her own murder covered up? It's because the motive for her murder is that she killed the best friend of the ones who killed her in turn, and solving the mystery would bring that to light.
- During Chapter 2's Mystery Labyrinth, each of the girls suspected of murder turn into Mystery Phantoms and get into different kinds of mutually exclusive arguments with each other. But remember how Shinigami explained that the phantoms' only purpose was to mislead people? The true relationship was none of the fights previously shown and all three were actually close friends working together.
Chapter 3: No Longer a Detective
- Makoto exposits about the power struggle within Amaterasu Corporation and how the Peacekeepers have overtaken everything. Shinigami points out he may work from within. Makoto is also introduced to the player in Kanai Tower, the tallest building in Kanai Ward - a place that seems suspiciously fitting for the topmost authority in the city. He's actually the CEO, as revealed by the end of the chapter, so of course he has internal knowledge.
- When meeting Yuma, Icardi is open to him joining because he is a detective and he likes how detectives work for anyone as long as the pay is good, finding them more trustworthy than people who talk big about fighting for the revolution. Icardi is the culprit of Chapter 3 who flooded the commercial district to pull off a bank heist and killed Shachi because he hated his idealistic views for fighting the Peacekeepers.
Chapter 4: The Imperfect Insider
- While discussing Dr. Huesca's security with Yuma, Makoto tells him that the fatal toxic gas was actually an accident of Dr. Huesca's, and he used it as part of his security system. There is nothing to counteract it either. As we find out in the following chapter, the defective homunculi he created were also an accident - and just so happened to be incredibly lethal as they also killed all of Kanai Ward's residents.
Other:
- It seems odd that if Yuma knew he was going to lose his memories when making a pact with Shinigami, why he didn't leave behind a Note to Self aside from a letter from the WDO and a train ticket. Especially since that doesn't seem to be against the rules of the pact. Unless his past self's plan required his future amnesiac self to know as little about his true identity as possible.
- On the Amaterasu Express, Yuma is able to sense Aphex and Pucci's fortes even though Shinigami hadn't fully taken root at that point. She also reacts with surprise when he first mentions sensing them to her. It's actually his Forte, not something he gained from their pact. This is also foreshadowed by him being able to explain Coalescence and not suffering any ill effects unlike explaining Shinigami and the Mystery Labyrinths.
- In Chapter 0, Shinigami dismisses Yuma's insistence of no one hiding in a bag by saying there's probably a Master Detective with the looks of a child and the mind of an adult out there. Ostensibly this is a Shout-Out to Detective Conan, but in retrospect she was also making a not-so-subtle nod toward Number One, who is the short and child-like Yuma.
- As Yuma starts to solve the Mystery Labyrinth of Chapter 0, he notes that he's not so much learning things as remembering them, and brings up the possibility that he might have been a high-ranking member of the WDO. He wasn't just a high-ranking member, he was the man in charge as Number One.
- Whilst investigating the first case, Shinigami gets annoyed at Yuma and wonders if he's even the same guy who sold his memories to her. Come Chapter 5, and it turns out Yuma and Number One having very different personalities is a significant plot point.
- On the rooftop, Yakou offhandedly mentions a rumour that the rain messes with people's bodies, one he doesn't believe is true. Said rumour was how the citizens explained away their pink blood and Yakou was right about the rain having no effect on their bodies.
- Upon Yakou showing him around the city, Yuma wonders how the city hasn't been flooded by all the rain, to which Shinigami says they probably have a good drainage system. Come Chapter 3, which not only introduces the flooded Dohya District, but also has Marunomon be flooded by Icardi sabotaging the waterworks.
- When Halara mentions that they looked up everyone beforehand including Yuma, Shinigami tells him not to worry about what Halara could tell him and that it doesn't matter. That’s because Shinigami knows everything Halara and Yakou know about Yuma is meaningless because our amnesiac “Yuma” isn't Yuma Kokohead, rather he's an entirely different person who stole his identity.
- When Number One first introduces himself and the other Master Detectives make a big deal out of him, Shinigami dismisses him as just some old guy. This is because she knows who the real Number One is, that being the much younger Yuma.
- When giving an Exposition Dump about Number One in the prologue, Desuhiko mentions that whenever Number One takes cases he always does them by himself, perfectly. This ends up being Makoto’s Fatal Flaw as he takes up saving Kanai Ward himself due to being Number One’s homunculus and thus thinking exactly like him and neatly explains why Yuma went as far as giving himself amnesia just to get himself to ask for help.
- Early on, Yakou asks Yuma to make him breakfast, having read in his profile that he's a great cook. After the meal turns out terrible, they blame it on Yuma's amnesia. It's actually because he's not the real Yuma Kokohead. Either that, or Yuma wasn't aware of Yakou's... dietary restrictions.
- To double down on this foreshadowing, if you paid attention to the loading screen trivia in Chapter 3 you may have caught the small seemingly arbitrary fact that states Makoto has his meals prepared for him due to lack of culinary skill. It would make sense that he and Yuma would share this trait considering Makoto is Yuma's homunculus.
- Early in Chapter 1, Yuma asks Shinigami what she knows about Number One, and Shinigami gets very evasive about it. Of course she does, she doesn't want to reveal that Yuma himself is Number One and the old man is a body double.
- Meat buns are stated many times to have become Kanai Ward's local delicacy after they were introduced a few years back and the citizens can't get enough of them. That's because they're the only things that can meet the nutritional needs of the homunculus population, due to being made from human flesh. Yakou often asks Yuma to buy them for him, and the first time asks for them specifically despite being desperately hungry, but none of the other detectives ever do. Which hints that Yakou is a homunculus.
- At several points in the game, you can have Yuma buy and eat a meat bun. Yuma thinks they're just okay — certainly not as good as everyone hypes them up to be — because he doesn't have the same dietary needs as everyone else. Shinigami, on the other hand, thinks they smell amazing. The other thing she loves the smell of is corpses.
- When discovering the Nail Man's most recent victim, Yuma is startled by the bloody body and asks Shinigami if what he's seeing is real. He was referring to the pink blood.
- Despite the series still keeping the murder victims' blood the Danganronpa hot pink, the blood on the door to the train's infirmary and from Shinigami slashing Yuma's throat is red. One of the differences between humans and homunculi is the color of their blood; all of the red blood we see throughout the game comes from Yuma, who turns out to be one of the only two humans we see bleed in the game with the other being Desuhiko whose nose-bleeding sprite has red blood due to him being an actual human as well.
- After Kurumi describes Karen to Yuma and he gets a good look at her, he remarks that she reminds him of himself. He's not wrong, since both of them had committed murder and gotten away with it.
- Shinigami explains that the Solution Blade is effective on anything in the Mystery Labyrinth, including the people he winds up bringing with him. Sure enough, during both Chapters 4 and 5, he has to use it against Vivia and Makoto respectively, who are not Mystery Phantoms, during the climax of the respective Mystery Labyrinths.
- If one looks closely at Number One during the flashback at the end of Chapter 2, his silhouette is clearly that of Yuma's raincoat. When he walks past the speakers it's also shown that he's about the same height as Yuma, instead of the decently tall old man who called the Master Detectives.
- When Yuma and Makoto are speaking about Number One at the start of Chapter 3, Makoto says to tell Number One that "his son is in trouble". While he plays this off as a joke, it may be a small hint towards him being Yuma's homunculus.
- At the end of Chapter 3, when Makoto gives the detectives their submarine back, Halara is concerned that their base might have become compromised. Their concerns are proven correct later on when Makoto fakes the call with Number One dying and the WDO HQ being bombed.
- At the beginning of Chapter 4's Mystery Labyrinth, Vivia Twilight reveals that after he independently learned of Shinigami's existence, Vivia did some research, discovering that the WDO's book vault had "The Book of Death" in its collection. The book had been taken, but only a handful of people have the clearance to even access the book vault, so Vivia dismisses the idea Yuma took it as he's a rookie. This only points to Yuma's pre-amnesiac self being someone with a rather high rank to access the vault. Someone like Number One.
- The owner of the underground ramen shop talks to a customer about how he had a hard time finding a way to sell his products to the people before finding a recipe that became a big hit. It turns out to have been due to the homunculi needing human flesh to survive. In the ending, he manages to become an even bigger success due to his recipe being a way for the citizens to feed themselves without resorting to cannibalism.
- If you look at Martina's profile after she is taken away to be executed, unlike other dead characters, there is no "X" on her picture. It can be assumed that it simply implies that Yuma thinks she is still alive, but the information in the actual profiles are not written in his perspective. At the end of Chapter 4, you find out that she is still alive, thanks to being saved by Makoto.
- Throughout the final chapter, Yuma comes across the remains of his zombie devoured friends, complete with bright pink blood stains. Not too long afterwards, he learns that the homunculi of Kanai Ward and the humans living outside have different colored blood, meaning it wouldn't make sense for the four human detectives to leave behind pink bloodstains. Sure enough, all of them turn out to be fine; Makoto simply imprisoned them in his penthouse and faked their deaths with the resources he had on hand in order to ensure he and Yuma would go into the Mystery Labyrinth alone.
- Whilst in the restricted area Kurumi gets separated from Yuma for an extended period of time. But despite none of the other detectives or Yuma himself being able to be around many of the zombies for very long without being attacked, she's completely fine when he meets up with her again. Indeed, in every scene where the defects are aggressive they go after Yuma, not Kurumi. After all, it is the nutrient makeup of human flesh that the homunculi instinctively desire.
- In the final Mystery Labyrinth, the Mystery Phantom blocking your path does not take the form of Makoto, as you might expect, but Yuma himself. But why would Yuma want to hide the truth from himself at this point? It's not until Makoto is unmasked that you realize that was Makoto's Mystery Phantom; it looked like Yuma because they share the same face due to Makoto being a homunculus based on his DNA. Yuma himself realizes this when the Phantom puts on a mask.
- If you stand right next to Makoto in Chapter 3 or 4 (or looked at each character's profiles), you might notice that he's the exact same height as Yuma, who up until this point has been far shorter than pretty much everyone else in the entire game. Another hint that he shares Yuma's DNA.
- While heading into Amaterasu Headquarters together, Yuma says he feels like he's being stared at and Makoto says that's natural with his face. No wonder given he has the same face as Makoto.
- At the start of chapter 1, Yuma points out that if Kanai Ward's Ultimate Secret is so important then obviously the World Detective Organization should have sent Number One in to look into it. They didn't, the real Yuma Kokohead swapped places with the real Number One, the former of whom agreed to let the latter use his identity, and Makoto is his clone, of whom is the one who sent the detectives to Kanai Ward, but the protagonist "Yuma" is the real Number One, having sent himself to investigate the case.
- Mid-chapter 3, Shinigami mockingly refers to Yuma as a "professional loner," much to his confusion. This makes a lot more sense in light of the reveal of his true self as the famously self-reliant Number One.
- The detectives repeatedly question why nothing they're doing while investigating Kanai Ward is leading them to "Kanai Ward's Ultimate Secret" and why they end up running around aimlessly with no answers. That's because it was a fabrication by Makoto Kagutsuchi to lure the Master Detectives to Kanai Ward in the first place for his plan to oust Yomi from power.
- In the final investigation, even though the labyrinth target is the criminals that Makoto kidnapped, the player is only given evidence about Kanai Ward itself and everyone in it being a homunculus because of Dr. Huesca's disastrous research in an attempt to rival the UG, and not enough about Makoto himself and his true identity, or why he kidnapped them. The reason for this incompletion is because Makoto himself didn't want Yuma finding out he was a clone of Number One of the WDO to be able to pin the crime on him, which would prevent Yuma from destroying the Mystery Labyrinth by reaping his soul, something of which Makoto takes advantage of for his Kill and Replace plan by entrapping Yuma (his original) there.
- Just prior to the reveal of his true identity, Makoto states that his procurement of criminals for Kanai Ward's food supply was done with the WDO's cooperation, in spite of the fact that he would never earn their cooperation for obvious reasons. Then it turns out the reason such an act was so easy for him is because he technically is the leader, being a clone of Number One. He'd have no issue getting their cooperation if he's a copy of their leader, after all.
- Shinigami explains that any outsider who does not make a pack with her will have no memories of the investigation when enters the Mystery Labyrinth and will have all memories inside the labyrinth to be erased when they exits the labyrinth. A subtle foreshadowing for the end when Yuma loses all his memories of Shinigami when he breaks the pact.
