In Virtuality Transcendent,
the reincarnations of Tom and Xiu who are all that survive of the ruined virtual afterlife awaken, through a series of intermediate virtual worlds, into robot bodies in the real world.
In Part 1,
Murdock and Annabelle are awakened from the nightmarish hellscape of Sphidia, recover their memories as Tom and Xiuying, and discover that they are still not in the real world.
- In Episode 1, Murdock and Annabelle stuggle to survive in the hell that the Queen thereof has made of Sphidia, until they are awakened inside the World Ring above a utopian Earth.
- In Episode 2, being told that they are suffering from side-effects of overuse of Virtuality, Murdock and Annabelle are helped to recover their memories as Tom and Xiuying.
- In Episode 3, Tom and Xiu begin to suspect that they are still in Virtuality and their therapist Metis is actually the Queen of Hell, and they ultimately bet their lives on it.
In Part 2,
Tom and Xiu are awakened into a dystopian Earth where they fight the automata oppressing humanity while recovering further memories that suggest that that world may still not be real.
- In Episode 1, Tom and Xiu are rescued from Virtuality by human soldiers on a dystopian Earth, who are fighting a war against automata trying to hide the terrible truth of reality from humanity.
- In Episode 2, while further recovering their lost memories of their time in Virtuality, Tom and Xiu begin to suspect that they are still not in the real world after all.
- In Episode 3, while joining the fight against the automata, Tom struggles to break through the blocks keeping him from accessing the "magic" of the virtual world he believes he is still in.
In Part 3,
Tom and Xiu struggle with the nature of reality itself before all is revealed to be a multi-layered deception helping them transition from Sphidia to the actual real world.
- In Episode 1, after succeeding spectacularly in breaking through the blocks on "magic", Tom finds himself in another world, where he is told that no "reality" has ever been really real at all.
- In Episode 2, Tom returns to the dystopian reality, where he teaches Xiuying to break through it just as he has, and she in turn convinces him to take their discovery less cynically.
- In Episode 3, while struggling to take having their reality turned upside-down in stride, Tom and Xiuying are eventually told the truth behind all these elaborate deceptions, and awakened for real.
- In Part 1, Murdock and Annabelle are awakened from the nightmarish hellscape of Sphidia, recover their memories as Tom and Xiuying, and discover that they are still not in the real world.