(9x08) Virtuality Transcendent: Part 3, Episode 2
Tom awakens in a hospital bed inside the underground rebel headquarters of the dystopian world. Doctors alert to his awakening, and call for their superiors, including Metis. They all want to know what the hell happened out there on the battlefield, how Tom came to be lying unconscious amidst the blasted ruins of the automata army. Tom insists to Metis that she knows already, but Metis pleads ignorance. Cynically, Tom explains the entire experience and even demonstrates magic to the rebel leadership present, who react with awe, which he treats as merely an act for his sake.
Metis expresses her belief that Tom may have somehow accessed whatever deeper secrets of reality lie behind the legendary "magic" employed by Keius Meij, the Ehrban who made her people immortal. She says that the means of her immortality is connected to the means of Keius' "magic", and that much of humanity have inherited a partial version of that means through her people's many offspring, so maybe, somehow, Tom has accessed previously-unknown features of that. The "goddess" he spoke with may, in turn, be none other than the Ehrban collective subconscious, which they worship as their goddess, Geie.
Released from the hospital, Tom reconvenes with Xiuying, the only person he's even vaguely sure isn't just part of an elaborate conspiracy against him, and tells her all about the experience, shows her magic, and confides his belief that they are still within a virtual world. He teaches her how to access magic through the mental blocks apparently placed on it in this layer of simulation, only for her to suddenly fall unconscious upon finally achieving it. But she finds herself "transcended" to the same other world Tom found himself in when he first achieved magic in this world, where she encounters the so-called "true goddess" just as he did.
Tom soon follows her there by force of will, suspecting that that happened. The "goddess" is glad that he has chosen to return, even if it is only temporary. She is very pleased that he has been able to pass his enlightenment on to Xiu, and expresses her hope that the two of them may be the vanguard for a reawakening for humanity, not only from the technological illusion in which most of them are now trapped, but from the metaphysical illusion behind which all of humanity have always been trapped. Xiuying is moved by these hopeful aspirations, but Tom remains cynical, and at his urging, the two of them return again to their bodies in the dystopian world.