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Date is an Esper
The Zero Escape series has involved Mental Time Travel, especially with Virtue's Last Reward and Zero Time Dilemma as prime examples of what an Esper can do. The reason Date remembers what happened in each route leading up to the Resolution route is cause he jumped back and forth between each one.

Hitomi has a mechanical arm wrapped in ABT in the epilogue
Virtue's Last Reward establishes the existence of mechanical arms and nerves as well as ABT, artificial skin that looks almost identical to the real deal, down to pores. Since Hitomi's moving her arm in the final dance sequence, this could actually be a hint she got it replaced to surprise Date.

The dancing ending isn't real
Actually, the whole part after Falco is knocked out is a hallucination, produced by Pewter and Boss cheer him up a bit. In particular, that means Aiba is still dead and Hitomi's arm doesn't work.

Pewter wanted to kill Date
He deliberately gave him Aiba instead of normal prosthetic eye to drive him insane and break him.
  • Heavily Jossed. Aiba was designed to keep Date stable seeing as he was in the body and brain of the Original Cyclops Killer.

Mizuki is a reincarnation of Manaka
We don’t know what Manaka was like when she was alive, and Renju and Hitomi where her friends. Therefore she was reincarnated into Renju’s daughter just to tie everything together.

Mizuki is part God or Kami
In Ota's route she mentions that her grandfather was born in the Ocean, actually born in the Ocean due to Great Grandmother being thrown overboard, and she was raised by dolphins. Date wants to call bull on that, but he admits there is something supernatural about her.

Mizuki is the Great Grand Daughter of Old Phi from Zero Time Dilemma
Phi was capable of similar feats plus had the same level of intelligence, same personality, and the same lovingly caustic relationship with her father figure. It would also link the game to the Zero Escape universe, smoothing over a few of the rough spots in the setting of the game. Plus it would be hilarious for Phi to realize her Great Grand Daughter is actually older than her.

Aiba's attraction to Date is wish fulfillment on Pewter's part
We know Pewter programmed Aiba, and we also know Pewter is homosexual. We also know Pewter's heart belongs to Renju, but it's fairly normal to be truly infatuated with one person you're attracted to and still fantasize in passing about other people you're attracted to but would never entertain the thought of actually dating. Date is fairly attractive, so it's not a stretch to think Pewter deliberately programmed Aiba to have a crush on Date as a tongue-in-cheek way of expressing his own attraction to him without personally indulging it.

This game takes place in the same universe as Zero Escape and Danganronpa
Shrug of God declares AI might possibly take place in the same universe as [1], but in a different timeline or era. If we take certain easter eggs as canon — which, admittedly, is a stretch — then we know Junko Enoshima and Gentarou Hongou were both patrons of the Matsushita Diner at some point. Given the sort of technology we see in [2], as compared to Aiba and the psync machine, we can infer it's been a long time between Zero Time Dilemma and AI, and therefore between 999 and AI, and, therefore, Hongou must have visited the diner when he was quite young. Given Enoshima's age at the time of her death, we can also infer Danganronpa: Trigger Happy Havoc definitely takes place after AI, at most 16 years after. We can guess the timeline is as follows: AI; next, Danganronpa, starting at most 16 years after AI; next, Zero Escape, starting probably around 30 years after AI.
  • Incorrect. 999 takes place in 2027, meaning that at most 999 is a decade post Somnium.
  • At the absolute earliest, AI takes place after 2013; Iris mentions Nelson Mandela dying that year in her route when the Mandela Effect is brought up.

Aiba was used to make Alter Ego and Zero III
Related to the above. I think it's fair to say Aiba is less technically sophisticated than Alter Ego, and Alter Ego is less technically sophisticated than Zero III. The apparent differences in sophistication are as follows:

  • Aiba has achieved self awareness and distinctive personality, but there are various hints that despite her high emotional and analytical intelligence in her own right, her social intelligence and likeness to a human mind leave something to be desired:

    • stunted, artificial-sounding speech patterns;

    • difficulty understanding other people's jokes, quips, intuition, and emotional state;

    • bizarre idiosyncrasies in formation of her own jokes and quips;

    • prudishness;

    • unwillingness to suspend disbelief.

  • Alter Ego is more humanlike than Aiba, but there's just something about him that feels off. There's some ever-so-slight deviation that serves as a constant reminder that he isn't the genuine article. Admittedly, it might just be the fact that he lives in a laptop.

  • Zero III possesses extraordinary social intelligence, probably more social intelligence than the average genuine human being. He is perhaps lacking in emotional intelligence, but this is clearly a deliberate feature of his personality design, since he is supposed to be the mastermind of a death game.

Given all this, and taking into account the timeline suggested in the above WMG, it's not a stretch to imagine the progression of AI quality from Aiba to Alter Ego to Zero III corresponded to a progression in available AI technology over time within the shared game universe. Alter Ego innovated over Aiba; Zero III innovated over Alter Ego.

Psyncing created the influx of espers that led to Zero Escape
Pertinent to the above two entries. It's possible the reason Date possesses some limited ability to shift from other timelines is because of his frequent involvement with the psync machine. His brain is accustomed to exchange of consciousness.

We know from Zero Time Dilemma that there is a hereditary component to ability to shift and its expression is controllable epigenetically. The amount of psyncing Date underwent may have activated his shifting gene due to the similarity of the stimuli, which would allow him to pass on his ability to shift to his offspring if he ever bore any.

Now suppose the existence of psyncing technology were leaked to the public at some point after AI. People may have been able to reverse engineer it or obtain access to it. If a sizable portion of Tokyo began psyncing, then, for epigenetic reasons, future generations would have stronger shift ability.

Akane Kurashiki claims the influx of espers that led to the events of Zero Escape occurred as humanity's defense reaction against the approaching timeline in which radical-6 would be unleashed on the world. It's therefore possible that Pewter possesses some weak shift ability, so weak he doesn't even realize it's there, and his foggy and vague intuition of the coming global disaster was what subconsciously led him to invent psyncing, as a sort of bootstrap to said defense mechanism. That is, though he didn't realize it, the reason Pewter invented psyncing was so that it would eventually be leaked, activate Tokyo's shifting genes on a large scale, and create generations of stronger espers to shift away from the radical-6 timeline.

Mayumi Matsushita will either have The Character Died with Him, or have The Other Darrin
It was sad news in July 2021 when Mayumi Matsushita's English VA, Philece Sampler, passed away. While her Japanese VA, Toshiko Sawada is still alive, they may just as likely Other Darrin her in the English version.

Mizuki was holding back against Saito in the climax.
Given that she's strong enough to casually kick down an entire tree, Saito should've been at least knocked out, if not outright dead, after Mizuki pummeled him in the head with her pipe several times. I can only assume this is because Saito's face is the one she had associated with Date for the entire time she's known him, so she ended up subconsciously holding back.

ABIS is secretly doing a cloning experiment and the guy who looks like Falco on the box is a clone of Date and the other Aiba is a prototype
The red herring here is that both the boy and Aiba are Date and Aiba from an alternate universe, but since this is Uchikoshi that would be too obvious of a twist.

The muscular dude on the cover is Ota
Dude's been working out

  • You mean the guy next to the bear...rat...mascot person? He looks too different to be Ota, even if he put on quite a bit of muscle. He might just be a different character.

Naix is a conspiracy theory... rooted in reality (if Zero Escape is canon to AI).
It's actually a sensationalistic version of Free The Soul from Zero Escape. A gold file in VLR mentions that Free The Soul was originally named "Free The Soul of Y", an anagram for "Left eye of Horus"... that is, Wadjet. In Zero Time Dilemma (set in 2028 of its timeline), an advanced quantum computer appears and is implied to be the first notable of its kind. In real life, we have created practical artifical intelligence before practical quantum computers. AI is apparently set in around 2019 of its timeline, therefore it is not a stretch to say that Free The Soul could have developed the Wadjet System.

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