With the discovery of Inflation Holes (something like wormholes) in the 24th century, humans can now travel the galaxy. At the space station "Watcher's Nest" is a relay point for ships equipped with Inlfation Drives. It is here that Misaki, a special ops trainee, is sent to battle the Ghoul. The Ghoul are a giant, alien race who are invading our universe from a parallel universe and their point of entry is the Inflation Hole at "Watcher's Nest". What are these Ghouls and why are they invading? What happened to Misaki on her trip to the station when she was attacked by a Ghoul? Will she and the members of her team be able to protect the station and the humans living on it with their special mecha units?
Misaki and her new team begin field training. When a friend from her future visits, the mission becomes much more real.
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.
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.
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.
Misaki travels to a time in which her father is still alive and is preparing to go to Watcher's Nest.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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