The crew of the Residential Ring find themselves back at Earth, except they are separated from Earth by a temporal barrier. When the crew discovers they are able to cross this barrier, they find that Earth is actually in a different time continuum. The task at hand; Seraphim must collapse the Inflation Hole to halt the invasion, even if it costs them their ticket home...and their connection to Misaki.
This episode begins with a flashback revealing Misaki’s childhood relationship with her father. The setting takes place in 2315, during the time Misaki begins her military training at boot camp.
Misaki, along with her new team, begins a field-training mission. The mission becomes surreal when a friend from Misaki’s time period arrives on the field.
Lyar traverses back in time to Feudal Era Japan in search of a ghoul. She is accompanied by a man who assists in her mission.
Meanwhile in Feudal Era Japan, Lyra encounters another spectral. This spectral is apparently Misaki….but in her ghoul form?!
Within the shadows, a bloody coup attempt is taking place in pre-World War II Japan. Kiri and Kotoko have been dispatched to quell the ghoul presence. Upon their arrival, Kiri finds that Misaki is already there and learns the cause of all the strange ghoul events.
Misaki travels to a time period, in which her father is still alive. Her father is in preparation to go to Watcher’s Nest.
Watcher’s nest meets another version of itself on another timeline. Suzanne and company travel to the second Watcher’s nest to investigate.
Misaki is in the quantum core, trying to hold back the Ghouls, and contacts the others. Suzanna realizes that she has has artificial memories placed inside her mind. Kiri hooks up to the integral system, in order to guide Lyar to Misaki.
LeBlanc contacts Woerns and his crew and reveals that it is now possible for the Ghouls to invade their universe through the inflation holes. Meanwhile, Misaki awakens and explains to Lyar and the others that the "other Misaki" (the ghoulish form) is still trapped, and was trying to hold back the Ghouls. But now the gateway has been opened and the Ghoul will be able to travel through not just the inflation hole at Watcher's Nest, but through all the inflation holes in the universe.
Misaki makes contact with her father's ghost. What became of Juzoh Kureha after the accident at Watcher's Nest comes to light. He and his friends encourter a Ghoul, and all of his friends are wiped out and he survives. Background information about Akari and Kureha's family life is discovered.
LeBlanc enters the same ruins as Mistaki and takes over the Integral System. Kotoko tries to hack into the system herself, but LeBlanc kills her when her presence is detected. LeBlanc frees a large Ghoul that has been sealed in stone at the center of the ruins. Manipulating the Ghoul, he attacks Misaki, who is still at the center of the ruins.
Misaki, Lyar, and Kiri return to the ruins to combat the giant Ghoul, which is under control by LeBlanc. Meanwhile, Kotoko carries Prim to the integral system interface, so she can hook up again. Misaki asks why LeBlanc wants to use the Ghoul powers to destroy the universe.
Misaki comes to Lyar in a dream and tells her that she wanted to change the past to avoid all the sadness and despair caused by humanity's interaction with Watcher's Nest. She was unable to change the past, but is able to give Lyar and the others an opportunity to alter the course of the future.