Fanfic / Encrypt within the Dark, to Save the Clockwork of a Heart

Encrypt within the Dark, to Save the Clockwork of a Heart is a Yu-Gi-Oh! VRAINS fanfic by Chyme set just after the finale of the anime.

A few months after Ai's demise and some tireless searching, Yusaku miraculously finds an amnesiac Ai floating around the network. Yusaku must learn how to deal with Ai's new, yet familiar personality, and Ai isn't making it easy as he tries to use Yusaku as his tool for his own ends. Adding to the problem are the rising number of rogue AI and someone called "Aniki" showing interest in Ai. Now, both must learn how to work together while trying to keep each other alive.

Currently sitting at 17 chapters and can be read here. Because this starts after The Stinger, expect a lot of spoilers for the anime.

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Tropes found in the fanfic:

• Amnesiac Resonance: Ai only has a few memories he can base himself on after his reformation, yet he is quick to put himself in harm's way to protect Yusaku, much to his own confusion. Yusaku remarks how he still has the same goofy personality even if Ai claims he's not the same Ai that Yusaku remembers.
• Awful Truth: Ai has a mental breakdown after he finally remembers he encrypted his own memories as a last-ditch attempt to prevent Roboppi from reviving him.
• Big Bad: There's someone called "Aniki" who kidnapped Aoi, thought to be the reason why many SOLTis suddenly gained sentience as the SOLTis follows his orders.
• Big Bad Duumvirate: It's later revealed that Queen joins forces with "Aniki" in collecting data from Aoi's torture to improve the Ignis Algorithm.
• Brain Uploading: Queen uploads her mind into the network to escape being hunted, but Roboppi outright says she's in too much pain from the transfer that she busts them out of prison to make it stop. Ryoken speculates she will slowly lose her humanity without the connection to her body. And it's discovered that she deleted parts of herself in order to make it stop, but it made her less human.
• Chekhov's Gun: Diamond Dust, the card Ai steals from a little girl proves vital in Yusaku's duel against Blue Maiden since it's the perfect card to counter water monsters.
• Cold-Blooded Torture: "Aniki" subjugates Aoi Zaizen in a mockery of the Lost Incident in a misguided attempt to format itself like an Ignis, preventing themselves from being overwhelmed by its programming again. Yusaku and the Knights of Hanoi, especially Ryoken, certainly didn't take it well once they found out.
• Continuation Fic: The story takes place just after the stinger of the final episode.
• Damsel in Distress: Aoi Zaizen was kidnapped by someone called "Aniki". Yusaku and Ai find her in LINK VRAINS but was forced to duel her before realizing they cannot save her as her real body is hidden somewhere.
• Dramatic Irony: Ai's grand plan of killing himself via splitting his data into the SOLTis bots in case he won the final battle. Now, many SOLtis start to gain sentience after some of his stray programming code incorporates into their software. He can't help but feel bitter at the irony of it all.
  Ironically the grand plan he outlined to Yusaku to get him to duel him properly, to send AI with free will into the world has come true!
• Everyone Has Standards: Ryoken still doesn't have a lot of love for Ai or any SOLTis, but he sincerely apologizes for using him to bait out Kitamura in an underground market for SOLTis sexbots to find Roboppi's location.
• Evil Tower of Ominousness: Since he's trapped in a virtual desert full of android corpses by "Aniki", Blood Shepherd creates one made out of Flame's data to lure in Ai and Playmaker.
• First Kiss: Yusaku and Ai share a passionate kiss in chapter 13, with a nonplussed Lightning watching on the sidelines.
• Fugitive Arc: Yusaku and Ai spend a few chapters laying low in the countryside when SOL Technologies began hunting down Ai for his supposed involvement with Aoi's disappearance.
• Hard Light: The Allure Queens attacking SOL Technologies are made physical with the improved Ignis Algorithm as they demonstrate by demolishing SOL Technology's main office. Ai observes this must be one part of Roboppi and Queen's plan from gathering data from Aoi.
• History Repeats:
  • Yusaku once again captures Ai who claims to have lost his memories. Unlike in canon, Ai really doesn't have any memories and isn't lying when he claims he's on a search for a way to unlock his memories.
  • Discussed in chapter 14 when they discuss how Queen's pride being destroyed is a reason for her actions just like how a hit on Go Onizuka's pride drove him to do dangerous and idiotic things that made things worse.
• Instant A.I.: Just Add Water!: Several SOLTis suddenly gain sentience and run away from their human masters to a shrine where they await more orders from "Aniki". Turns out it was Ai's fragments acting like a Contagious A.I. to all SOLTis bots it goes into, and this gives the bots some semblance of free will that Roboppi took advantage of.
• Insult Backfire: Ai taunts Spectre that he should return back to Revolver like a dog he is, the latter takes it as a compliment before returning a jab about Ai's true loyalties.
  Spectre: Thanks for the compliment. A dog is exactly what I am; I would never turn against him.
• Just a Machine: Ai compares the modified SOLTis as empty hardware at worst and little more than animals at best at Ryoken's provocation.
• Killed Offscreen: Queen's body was found lifeless after the fiasco with "Aniki". Turns out Queen is still alive the next chapter via uploading her mind in the network.
• Lap Pillow: Ai lets Yusaku sleep on his lap twice, the first after a tiring ordeal with "Aniki" and after SOL Technologies captured "Aniki". Chapter 10 is even titled after this.
  Ai: Here! Delight in the softness of my lap-pillow!
• Let's You and Him Fight: Roboppi defeats Revolver and Blood Shepherd offscreen and turns them into statues, then forces Blue Maiden and Spectre to duel each other in order to release one of them.
• Laser-Guided Amnesia: In the first chapter, Yusaku finds an amnesiac Ai who lost, or more accurately, doesn't have access to his memories for an unknown reason. He even lets Pandor scan his biometrics to prove he's not pretending to be an Amnesiac Liar again.
• Loss of Identity: What essentially happens with Ai during the start of the story. He knows from his few fragmented memories that he had a close connection to Yusaku, still acts like his goofy self, but feels he isn't complete and unsure why he would partner up with someone like Yusaku.
  Ai: It’s like part of me is encrypted and I can’t hack into it. There’s no real way to know if I’m fully formed, or if I’m missing parts of myself I once had. I’m functional, sure. But I don’t remember you. And there are parts of myself I can’t access, that I’m blocked off from, that I can’t hack. It’s annoying. Maybe those are my memories? But then there’s no logical reason why I shouldn’t be able to access them.
• Manipulative Bastard: Yusaku outright muses Ai as this:
  He really is a manipulative bastard, Yusaku thinks. Utterly shameless about using him – if it hadn’t been for that recording of the duel with Bohman, with Yusaku reacting so emotionally to his death, would he even have bothered coming back to him?
• Mercy Kill:
  • Ai dismantles all the data of the broken and discarded SOLTis bots he and Playmaker encounter in the virtual desert out of pity.
    'Bye-bye,' he intones humourlessly, watching the last of the data glitter and disappear. 'Maybe you'll be happier like that; at the very least you won't feel any more pain.'
  • In chapter 15, Ai gives a digitized Queen a quick death to stop her pain-induced rampages even though Yusaku, who is nearly absorbed in her and understands that she's too far gone, is unhappy that he's the one to do it.
• Moment Killer:
  • After a few failed attempts in the hot springs, Ai ramps up his enticement game with Yusaku nearly falling into Ai's seductions, then Ryoken bursts into the room.
  • Lightning, or a Virtual Ghost of him disturbs Yusaku and Ai's intimate moment after watching them making out for an uncomfortable amount of time.
• Mortality Phobia: Yusaku realizes that Queen's actions comes from being afraid to die, stemming from watching her grandmother's dying reaction. It was this fear that made her do desperate things to survive, like uploading her mind in the network and attempting to merge herself into Yusaku's mind.
• Mythology Gag: Diamond Dust, a card Rio used in Zexal, appears in Yusaku's duel with Blue Maiden.
• Near-Villain Victory: Once again, Roboppi is about to win his fight but Ai unleashed the virus building up in him, giving Blue Maiden time to interfere with an illegal card to stop the duel.
• Quest for Identity: The story starts with Ai's quest to find his missing memory data while pulling Yusaku for a ride.
• The Reveal: "Aniki" is actually Roboppi, who inexplicably survived their death and now wants to revive Ai and take care of him his own way.
• Robosexual: The fic explores how Yusaku and Ai's new partnership affects their dynamic and feelings while trying to keep each other out of trouble. After Ai's memories came back, they both quickly admit their true feelings for each other and even consummate their relationship after running away from everyone else.
• Sexbot: Characters note that there is an underground market for SOLTis sexbots, as SOL Technologies is unwilling to make one so illegal suppliers do some unauthorized modifications down there. Kitamura is revealed to be running one after he's fired from SOL Technologies.
• Shout-Out:
  • Word of God says Chapter 4 has a scene that is inspired by My Next Life as a Villainess: All Routes Lead to Doom!, likely the tree climbing scene.
  • Ai orders Yusaku that he should fall for him than he already has.
• Take That!: The stinger at chapter 13 takes a swipe on the Allure Queen archetype's useability in the card game:
  Another, an avid player of Duel Monsters, snorts. 'Lame,' they declare. 'They should have used better monsters. Allure Queen is such an unworkable archetype.'
• The Tease: A tactic Ai cunningly (or so he thought) uses to manipulate Yusaku into falling for him, planning to influence him with affection to bring out his protective instincts. Yusaku actually knows what he's doing and, while he doesn't reciprocate any teasing, he lets Ai do so to prevent him from running away. In an ironic twist, it was Ai who falls for the other when Playmaker used a joke card he gave him to win the duel.
• Virtual Ghost: Playmaker stumbles upon Lightning's copy in LINK VRAINS, who puts one copy in the off-chance of someone searching for the Cyberse World ruins after his death.
• You Owe Me: Yusaku banks in SOL Technologies's debt of him saving LINK VRAINS many times as one of the reasons they should stop following Ai, which gives them enough time for them to leave Den city before the police raid his apartment.