In the Year 20XX AD at Lake Turkana,Kenya,an archeological excavation is underway,led by Doctor Masuda. They found a cross-shaped indentation at the shore of the lake. When Masuda placed the shape into the silver tablet,It rise up an underground ruins.
4000 years later,Shion Uzuki was testing on an android,KOS-MOS aboard the Woglinde when the crew retrieve a Zohar Emulator,one of thirteen replicas of the Zohar. Shion begun seeing a vision of a young girl. Cherenkov monitors Shion's progress,but is also a U-TIC spy furthering their goal of finding the original Zohar. As the Woglinde is attacked by Gnosis,KOS-MOS self-activates and saved Allen Ridgeley,but accidentally killed Luis Virgil. Lieutenant Caspase & Captain Moriyama are killed while the crew escaped,but Cherenkov has been infected. They were picked by the Elsa Crew led by Captain Matthews. One surviving Gnosis infiltrates in,but was stopped by Chaos.
Later,a cyborg,Ziggy is sent to extract MOMO from U-TIC, as data stored inside her could open the way to Miltia, lost in a disaster for which her creator Joachim Mizrahi is blamed. They quickly escape from the attacks by Margulis. Albedo,who is working with U-TIC for his own goals,sets out in pursuit of MOMO.
Shion reveals to Chaos & that She & her boyfriend,Kevin Winnicot are working on a KOS-MOS project. Until the U-TIC soldiers attack & she manage to get the project to safety,but was forced to leave Kevin behind. Ziggy & MOMO are ambushed by the U-TIC ships. They manage to lose them & are saved by the Elsa crew. Cherenkov somehow mutated & attacks the crew. Ziggy was forced to kill him when he tried to kill MOMO before they were rescue by Gaignun Kukai,commander of the Durandal.
They travel to the Kukai Foundation base above Second Militia,operated by Gaigun's brother. They retrieve the evidence from KOS-MOS' memories. Inside of it,The group met Nephilim,a girl from Shion's vision. They also met the vision of Febronia,a realian woman killed in the Militia conflict,who asked them to free her sisters. After fulfilling their mission,Nephilim tells them that KOS-MOS was designed to stop the energies of U-DO from entering reality. MOMO was captured by Albedo. As the fleet try to destroy the base,Wilhelm,who has secretly observes,arrives & protect the base.
The group saves MOMO while Shion & KOS-MOS fights with Albedo & the Blue Cloaked Man. After getting defeated,Albedo summons Proto Merkebah to destroy the base before fleeing. The Blue Cloaked Man,who turned out to be a resurrected Virgil,fled. Shion's group managed to stop it before escaping. During the Aftermath,Shion vows to stop U-TIC.