Following her resignation from Vector in the wake of her discoveries and the Gnosis Terrorism, Shion allies with underground group Scientia to investigate. Her former co-worker Allen takes her place looking after KOS-MOS. Meanwhile, Canaan, Jr., Jin, chaos, MOMO and Ziggy are investigating a landmass that originated from Lost Jerusalem.
They are attacked by Margulis, then the landmass is swallowed with the Elsa in an inverted pocket of hyperspace. Shion meanwhile visits Allen, and sees the demonstration of two new weapons for fighting the Gnosis — T-elos, a battle robot meant to replace KOS-MOS; and Omega, a mech created from the Proto Omega's remains and piloted by Abel.
After the test, T-elos' creator Roth Mantel informs Allen that KOS-MOS will be scrapped so development can focus on T-elos. As KOS-MOS's weaponry is the only way to break into the hyperspace pocket and save the Elsa, Shion leads the group into the facility and rescues KOS-MOS, guided at one point by Abel. During this time, Shion has frequent visions of the girl Nephilim, and has blackouts where she is contacted by U-DO. Events are also observed by Wilhelm, who is working with the Testaments to find both Abel and Abel's Ark.
Entering the hyperspace pocket, the group find the Elsa and investigate the area, encountering both Albedo and Virgil and learning that the Vessels of Anima powering their E.S. mecha are key to the Testaments' plans. They are then confronted by Mantel — who reveals himself as the Red Testament — and T-elos. T-elos almost kills KOS-MOS, but Shion's pendant activates, apparently transporting them to the planet Miltia fifteen years into the past, which is revealed to be a world within Shion's subconscious.
They are attacked by Voyager, who is beaten back by a redesigned KOS-MOS. During the group's time there, Shion learns the true events that caused Miltia's fall; her father, Kevin, Margulis and Mizrahi were attempting to control the Zohar through experiments involving both Shion and her mother, but when U-TIC and Federation forces clashed, Kevin and Margulis released unstable combat Realians which slaughtered nearly everyone in the battle.
The trauma caused the young Shion to resonate with the Zohar, summoning the Gnosis and awakening U-DO; it was only Mizrahi's self-sacrifice in sealing away Miltia that prevented the chaos from spreading.
The group fight Virgil before he is calmed by the spirit of Febronia — who tended him when he was injured on Miltia and with whom he formed an attachment prior to her death — and follows her into the afterlife. The Red Testament also appears, revealing his true identity as Kevin and asking Shion to join him.
(Continued in Also sprach Zarathustra)
(Excerpt from an online resource regarding Episode III's plot. View original source.)
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