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, in reality 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 which stalled U-DO's spread. 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.
Evading Kevin and T-elos, the group escape from Shion's subconscious back into the normal world, but following this Shion becomes emotionally unstable. During their absence, the Federation government is manipulated by Yuriev into assaulting Ormus in search of an artifact called Zarathustra. Abel's Ark, summoned by the events in Shion's subconscious, appears in the real world and begins causing planets to vanish as it pursues Zarathustra. Nephilim asks Shion to free Abel from Yuriev's control, then Yuriev leads the Federation fleet and Omega to capture the Durendal. Yuriev activates the Zohar Emulators stored in the Durandal, intent on using them in combination with Omega and Abel's Ark to defeat U-DO by rising to godhood. The group successfully infiltrate Abel's Ark, where Jr. kills Yuriev with help from Albedo. Albedo then teleports Abel and the Zohar away. The conflict results in Albedo's consciousness merging with Jr., while Gaignun dies along with Yuriev. The group follow Abel and the Zohar to the planet Michtam, the holy land of Ormus. There they kill a disillusioned Margulis, and Canaan sacrifices himself to destroy Voyager.
Descending deeper into Michtam, Shion experiences visions of Lost Jerusalem, seeing chaos under the name "Yeshua" alongside a previous incarnation of herself, KOS-MOS's physical template Mary Magdalene, and Jesus prior to his death. In a final confrontation with T-elos, they learn that T-elos and KOS-MOS were both designed by Wilhelm and the Testaments to resurrect Mary Magdalene, with KOS-MOS holding her spirit and T-elos being made from her body. The group are then confronted by Kevin, who asks KOS-MOS and Shion to join him. Shion, blinded by her love, joins him until Allen convinces her otherwise, voicing his own long-held love. The group then confront Wilhelm at Zarathustra's resting place. Wilhelm reveals that he has been preserving the universe from ending due to human wills that reject connection with U-DO; by capturing U-DO's "eyes" Abel and Abel's Ark and using eternal recurrence, Wilhelm has trapped the universe in a time loop with the power of Zarathustra and the Zohar. The Gnosis are revealed to be spawned from the wills that reject U-DO and escape from U-DO's realm. Shion, whose necklace and will are key to activating Zarathustra, is tortured by Wilhelm in an attempt to make her wish for recurrence. KOS-MOS shatters the necklace, preventing the recurrence from ever happening. A redeemed Kevin then sacrifices himself to destroy Wilhelm, allowing the group to cripple Zarathustra.
Abel, Nephilim, KOS-MOS and chaos choose to stay on Michtam, drawing all Gnosis to them and using a dimensional shift to move that region of space to Lost Jerusalem. Their actions and the release of chaos's Anima energy—which is accelerating the universe's death—will delay the universe's destruction, giving Shion time to find Lost Jerusalem and discover the key to changing humanity's will and saving the universe. During the escape, Jin returns to help chaos and KOS-MOS and dies fighting off the Gnosis. The resultant explosion of energy from the dimensional shift destroys the U.M.N., rendering faster-than-light travel impossible. Shion goes with Jr. and Allen on the Elsa to find Lost Jerusalem, while MOMO stays behind with Ziggy to reconstruct a new travel network with Scientia's help. In the mid and post-credit scenes, a badly damaged KOS-MOS floats through space and is contacted by chaos, saying they will both awake when they are needed. KOS-MOS is last seen drifting towards Lost Jerusalem.
