Misaki is implanted with a microchip in her head and synchronises with an artifical intelligence which allows her to observe an on going fight in the Quantum Core. Meanwhile, Earth has no idea what is going on at the Watchers Nest.

This episode is set two months before the events of episode one. A shuttle is transporting four new cadets to the Watcher's Nest but on route the vessel is attacked by a Ghoul. It is then up to Misaki to defeat the alien and save her colleagues.

The cadets continue their training and as usual Misaki is terrible, that is until the training switches to live rounds and her true potential is revealed. However, an accident with her thrusters during another exercise leaves her in danger.

Misaki and the other cadets are given a day off. However, when a Ghoul turns up in the center of town Misaki must once again deal with it.

A reporter from Earth has come to the Watchers Nest. As such the crew must try to keep him away from any classified information. However, when a training mission goes awry he may find out more than he is meant to.

After more intensive training, Susana decides that she can no longer continue at the Watcher's Nest. Because of this she quits and has the last two years of her life erased.

Bernard continues to search for information after his failed memory wipe and he manages to persuade Misaki into helping him. However, when they act on that information things start to get dangerous and Misaki is trapped in the Quantum Core.

Misaki is rescued from the Quantum Core by the Lieutenant, but no sooner does she wake up in hospital than she is being used in yet more unusual experiments.

The cadets have finally graduated and Lyar is given a promotion but their new roles keep the group separated. As such Misaki is struggling to cope with frightening hallucinations and has nowhere to turn.

After Ruxandra is killed in a Ghoul attack because of a lack of available soldiers Misaki blames herself. Afterward, Misaki starts suffering from visions of her dead friend.

Since the last episode the Ghoul have been attacking the Watcher's Nest almost continuously. However, in some rare down time Misaki decides to visit her father's tomb and learns some truths along the way.

The Ghoul are attacking again but this time in force. As such all of the available soldiers are dispatched to keep them at bay. During the battle Misaki once again transforms and is captured by her commanders. The truth about the numerous experiments is finally revealed.

Misaki is under the full control of the commander who sends her into Battle alone. However, in the Quantum Core things take an unexpected turn and time is rewound 3 years back to the Military Academy on Earth.

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.