The first episode begins with a flashback to Misaki's childhood depicting her relationship with her father. Back in 2315, Misaki is just starting her military training in boot camp.

Misaki and her new team begin field training. When a friend from her future visits, the mission becomes much more real.

Lyar travels back into feudal Japan to find a ghoul. She meets a man who helps her complete her mission.

Still in feudal Japan, Lyar encounters another spectral that appears to be Misaki in her ghoul form.

A bloody coup attempt is taking place in pre-World War II Japan. The team is alerted to a ghoul presence in the middle of that coup and Kiri and Kotoko are dispatched to attack it. When they arrive, Kiri finds that Misaki is already there and learns about what has been causing all of the strange ghoul events.

Misaki travels to a time in which her father is still alive and is preparing to go to Watcher's Nest.

Watcher's Nest comes into contact with a version of itself on another time-line. The team, including Suzanna, travels to it to gather information.