Faced with Albedo and his ES Simeon, now merged with the Kirschwasser, Shion sends KOS-MOS to rescue MOMO's sister. But even if they stop Albedo, can they stop the Ten no Kuruma from crashing into Second Miltia and destroying it?
Albedo takes advantage of the confusion to kidnap MOMO, right in front of Jr. Meanwhile, Shion is dealing with KOS-MOS having killed Lt. Virgil. Back on the Durandal, Gaignun reveals his and Jr's connection to Albedo, and what Albedo wants with MOMO.
The Foundation and Second Miltia cleared of charges, the party is still dealing with the memories that were brought up. Meanwhile, Albedo is making plans of his own, by using the Song of Nephilim to summon an army of Gnosis to attack.
Within the Encephalon, Shion and Jr must each face demons from their pasts; Shion, the death of her parents; Jr, the loss of his brother. While Nephilim forces them to accept the past, and shows them a possible future that is to come, chaos and Jin fight against Pellegri and her ES Issachar.moreless
With the Durandal accused of attacking the Woglinde, Shion and the others are under arrest. The only way to clear their names is to provide proof of what really happened, from something with AAA-class protection. And the only way to get that, is to do an Encephalon dive into KOS-MOS' unconsiousness.moreless
The Elsa still under attack from the Gnosis, the Durandal comes to the rescue. Before much could happen, KOS-MOS defeats the Gnosis by sucking them into herself. While the Elsa docks with the Durandal for repairs, Jr, captain of the Durandal and co-director of the Kukai Foundation, gives the party a tour of the ship.moreless
U-TIC, the organization whom Ziggy rescued MOMO from, comes after the Elsa, intent on getting her back. However, when they are damaged in hyperspace and have to gate-out, they find themselves surrounded by a large armada of Gnosis.
Aboard the Elsa, KOS-MOS, Shion, Allen, and Virgil meet with another set of passengers aboard the ship, the cyborg Ziggy and the prototype Realian MOMO, as well as the crew of the Elsa; Captain Matthews, Tony, Hammer, and chaos.
The Woglinde heavily damaged and under attack from the Gnosis, KOS-MOS activates to protect Shion. While Shion escapes the Woglinde in an escape pod, KOS-MOS gets herself picked up by the freighter Elsa.