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The What If series by Meridian1 is an AU version of The Matrix starting mid-way through the first film. When Cypher successfully kills Tank on the Nebuchadnezer and then pulls the plug on Neo, he reveals that part of the deal he made with the Machines included sparing Trinity to be his wife in his new reality. However, a few months later, ‘Thalia Reagan’ is contacted by the still-living Neo, who reveals her true past to her and his own current status as a glitch in the system, as the two resume the war against the Machines.

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The series consists of two stories; What If and The Return of What If, depicting an alternate end to the war against the Machines.

The What If Series contains examples of:

  • Abhorrent Admirer: It’s unclear to what extent this applied to Cypher before he betrayed the rest of the crew, but after his treachery and subsequent ‘reprogramming’ of Trinity she only stops Neo from killing Lloyd in a later confrontation because Lloyd genuinely didn’t know what he’d done.
  • Amnesia Missed a Spot: Thalia Reagan consciously remembers nothing of Trinity’s life, but she experiences a recurring nightmare of watching Neo ‘die’ when Cypher pulls the plug, and swiftly finds herself aware of what to do once she starts hacking again despite having no conscious memory of Trinity’s skills; Lloyd himself experiences a few dreams of Cypher watching Trinity, but never realises their significance.
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  • Amnesiacs Are Innocent: To a degree; Lloyd might be a fully developed human being, but Thalia/Trinity argues that Neo shouldn’t kill him because Lloyd genuinely doesn’t remember committing any of Cypher’s crimes (although he ends up killing Lloyd anyway when an Agent takes control of Lloyd’s body).
  • Ascended Extra: In the absence of the Oracle, Neo and ‘Thalia’ are aided by Natalie, one of the Oracle’s potentials and the only one to survive the attack on her apartment.
  • Back from the Dead: Neo initially pulls this off by transferring his essence into the Matrix after Cypher pulled the plug, allowing him to exist as a ‘glitch’ in the system, but takes it to the next level in The Return when he transfers back into his recovered body in the real world.
  • Badass in a Nice Suit: Averted in The Return, when Neo’s actions force the Machines to deploy a new type of Agent who are better able to understand humans on an emotional level, to the point of dressing in more casual clothing.
  • Bittersweet Ending: Applies to both stories;
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    • In What If, Trinity’s memories are restored and the human resistance has begun to rebuild in the real world, but Morpheus and the Oracle are dead, Zion has been decimated, and Neo is essentially trapped in the Matrix.
    • In The Return of What If, the humans have defeated the machines and Neo has been restored to his body, but they had to kill virtually everyone connected to the Matrix to achieve victory.
  • Chekhov's Gun: The Return opens with Cairo, one of the new Agents, deploying the Sentinels to find something in the real world; later in the fic, it is revealed that they salvaged Neo’s body, which was never ‘recycled’ after his ‘death’ but just kept on a form of life support until the appropriate programs worked out what to do with him.
  • Code Name: As in canon, those freed from the Matrix tend to adopt their hacker aliases in the real world (with the exception of the Oracle’s former ‘student’ Natalie); it also reveals that Trinity and Cypher’s original names were Thalia and Lloyd.
  • Curb-Stomp Battle: By The Return, the machines have recognised that, while it was once seen as impossible for any human to survive a fight with an Agent, it is no considered impossible for any Agent to survive a fight with Neo.
  • Deal with the Devil: In The Return, the special reserve Agent Cairo attempts to offer Neo one of these by giving him the only thing the Machines can give him; his original body.
  • Death by Adaptation: The initial divergence from canon is that Tank is killed by Cypher’s betrayal, which leads to Morpheus’s death after the Agents break him and get the access codes to Zion. It is also all but explicitly stated that the Agents killed the Oracle.
  • Demoted to Extra: In contrast to his role as Neo’s Evil Counterpart in the original films, in What If Smith is killed/destroyed in the final battle and never returns.
  • Disability Immunity: Basically applies to Neo from the Machines’ perspective; as a glitch in the Matrix without access to his body, he can’t actually take any form of sustenance, and must make a conscious decision to come in contact with anything, but this also means that the Machines can’t even try and hold him prisoner unless he lets them, and he eventually learns how to fight the Agents.
  • Fate Worse than Death: The moment Trinity learns that Cypher intends to leave her alive and ‘reprogrammed’ to be his wife when he’s returned to the Matrix after he kills Neo and the rest of the crew, she starts praying that he’ll trip and pull her plug rather than live a life like that.
  • Godzilla Threshold: By the time of the second fic, Neo has proven to be such a threat that the Machines have opened the ‘special reserves’ file, consisting of a very atypical set of programs that defy all standard parameters of Agents.
  • Identity Amnesia: Arguably applies, as Cypher and Trinity have been programmed back to their ‘original’ identities of Lloyd Reagan and Thalia, forgetting their lives in the real world.
  • Jacob Marley Apparel: Essentially applies to Neo, who apparently cannot change out of the clothes he was wearing when Cypher pulled the plug, although he muses that the outfit actually isn’t that bad and he can at least make it look cleaner.
  • Jerkass Has a Point: To a minor degree; in The Return, Trinity takes Cypher’s rants about Morpheus into account when making her own ‘pitch’ to potential recruits, ensuring that they understand at least some of the potential problems they’ll face if they take the red pill while still promising them the truth.
  • Karmic Death: After all of Cypher’s efforts to get back into the Matrix, Lloyd is killed when he falls victim to the fate of anyone trapped in the Matrix and becomes the host for an Agent that is subsequently killed by Neo.
  • Killed Offscreen: It’s never specified what happened to the Oracle, but all evidence makes it clear that she was killed by the Agents after they broke Morpheus and learned what he knew.
  • Legacy Character:
    • Neo and Trinity basically see themselves as doing this for Morpheus’s memory, to the point that The Return sees Trinity become the captain of the second Nebuchadnezzar.
    • Also arguably applies to Natalie, one of the Oracle's potentials who essentially takes on her teacher's role after the Oracle is killed by the Machines.
  • Lesser of Two Evils: The series essentially builds to the moment when Trinity must decide whether to destroy the Matrix (and thus destroy Neo) or keep the war going and spare him; only the rediscovery of Neo’s original body gives Trinity a third option by allowing him to download back out of the Matrix before she destroys it.
  • Living Emotional Crutch: Neo explicitly muses that the knowledge that Trinity survived Cypher’s betrayal was the only thing that stopped him going insane after he realised his new existence as a glitch in the Matrix.
  • Meaningful Name: Natalie telling Neo that Trinity is waiting for him serves as a sign that Thalia has remembered her past.
  • Nice Job Fixing It, Villain!: In The Return, Cairo attempting to bribe Neo by restoring his body removes the last true issue Trinity had with destroying the Matrix by allowing Neo to return to his body.
  • Oh, Crap!: In The Return, Cairo has one when she realises that Neo has used her link to his body to download himself out of the Matrix, leaving Trinity with no real reason not to destroy the system.
  • Only Known by Their Nickname: While he learns Trinity’s original name of Thalia, Neo still thinks of her as Trinity, and Trinity herself chooses to return to this alias once she is freed from the Matrix again.
  • Prophecy Twist: Neo initially assumes that this is the reason for his continued survival; as the Oracle predicted that he or Morpheus would die, he was essentially transformed into a glitch in the Matrix so that one of them would ‘survive’.
  • Reality Ensues: In The Return, the freed humans choose to destroy the Matrix because there is literally no way to free everyone in it; at best half of the people in the Matrix would accept the idea that they’ve been living in a dream, and the Machines calculate that only twenty percent of the overall population of the Matrix would be able to cope in the real world without just going insane or reacting like Cypher, and that’s without taking into account the lack of resources on the decimated Earth to sustain a population of that potential scale.
  • Saying Too Much: In The Return, Neo and Trinity provoke Cairo into this by denying her claim that she has found Neo’s body, tricking her into giving them proof that Neo’s body is real and alive so that Neo can transfer himself back into his body.
  • Single Woman Seeks Good Man: In a flashback to Trinity’s early observations of Neo, she muses that she likes him because, during his hacking activities, Neo tends to take money from drug dealers and the like more than he takes it from honest people.
  • Spared by the Adaptation: Unlike in canon, Neo and Trinity survive to the end of the war with the Machines.
  • Swapped Roles: The story opens with Neo and Trinity having essentially swapped roles from the original film, with ‘Thalia Reagan’ now ignorant of the truth and Neo having to restore her memory of her life as Trinity and the existence of the Matrix.
  • True Love Is Exceptional: For unexplained reasons, even in his ‘glitch’ state, Neo can still feel everything when he makes physical contact with Trinity.
  • What Could Have Been: Towards the end of both fics, Trinity experiences brief flashes of what would have happened in the original film, but decides that she is content with her current reality.
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