The future is uncertain for Yuuji, Amane, Makina, Sachi, Yumiko, and Michiru. As it turns out Yuuji's life is far more complicated than anyone could have imagined. He soon finds himself entangled in a political war within CIRS while the school is on the brink of closing. One thing is for certain, though—the girls are not who they were a year ago and will no longer let anyone take things away from them. With help from a new mysterious individual, they may just be unstoppable.
Yuuji’s meeting with JB continues and he discusses what his life was like under the care of his master, Asako.
As Asako's health begins to interfere with her work Yuuji covers for her and in doing so finds his path in life.
As Yuuji follows the same path as Asako, his military life causes him to forge deep bonds with those around him.
While Yuuji is away, Asako’s condition worsens, but her final words aid him to move forward. He’ll need to remember that message as a shadow from his past reappears.
Yuuji is gone and the media is portraying him as a terrorist! While trying to discover where he is, the girls must say goodbye to Mihama Academy as they start another journey.
The girls procure a new “dorm” while searching for a way to rescue Yuuji. Strangely, help may be only a phone call away.
The girls’ interests correlate with those of the disembodied Thanatos, and they begin to organize for their mission.
The mission begins! But even with the nearly all-knowing Thanatos, rescuing Yuuji may prove problematic.
As the girls ready the ship for travel and continue Thanatos’ plan, Yuuji reunites with more than one special person.
Combating the very mindset drilled into him by the man, Yuuji sets out to face Heath Oslo.