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 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.
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 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.
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.
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.
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 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.
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