It all comes crashing in
The only other surviving URTV, Albedo, is in league with U-TIC. Together with Margulis, the commander of the U-TIC, and his female subordinate Pellegri, they hatch a plan to frame the Kukai Foundation for attacking a U-TIC cruiser without provocation. To prove their innocence, Jr. enlists the help of Shion to use KOS-MOS for an Encephalon Dive - a virtual reality simulation of their collective memories - to unlock the protection on the real footage of the events in the general database.
While in the Encephalon, the characters relive the memories of the Miltia Conflict and witness the apparent suicide of Joachim Mizrahi from his fortress, the Labyrinthos. While Jr. relives the horrors of the events that wiped out of the URTVs, Shion is haunted by memories of her sick mother being murdered by a strange variant of the combat Realians. At the end of it all they find Febronia, a Realian who lived in a church on Miltia, who looked after Shion when she was a child. Together with Nephilim she explains that KOS-MOS is the only hope that stands between the power of U-DO and the potential destruction of the universe. They find themselves in an ancient tomb that seems familiar to KOS-MOS, as she wakes up from hanging on a stone cross.
As the truth of the U-TIC cruiser incident is revealed, Albedo unleashes the Song of Nephilim - another powerful relic left over from Joachim's research on Miltia. The huge reverse pyramid structure projects a haunting sound wave that summons Gnosis en mass. In the chaos, Albedo swiftly kidnaps M.O.M.O. from the Kukai Foundation and attempts to extract the hidden data from her. Jr. leads the team to rescue her and stop the Song of Nephilim... but after rescuing M.O.M.O., a mysterious blue-cloaked figure appears, allowing Albedo to get away and activate yet another toy from the Miltia Conflict - the floating fortress Proto-Merkabah.
With the fate of the entire planet of Second Miltia at risk, the entire party is forced to invade the fortress and stop Albedo once and for all. Prepared to face his brother on his own terms, Jr. unleashes his Red Dragon aura and defeats Albedo, but thanks to his amazing regenerative abilities, Albedo once again escapes. As the pieces of Proto-Merkabah shower onto Second Miltia, the Elsa crash lands safely on the planet, concluding the first episode.