When Mari Wakatake arrives at the gate of the exclusive Kaihou Academy, she is a girl without a past. Five years earlier, SOMETHING happened to her. Something that took the lives of her parents and every other human on Kamioki Island, then wiped her mind clean. But if Mari’s past is an unknown nightmare, her future may soon become even more terrifying. Because while she was the sole HUMAN survivor, there is something else that lived through that same night, and her path is about to cross Mari’s again. Something in a female skin has invaded Kaihou Academy, and Mari is its target. The subjugation of Earth has begun, and the heart of one young woman may be the key to our race’s ultimate salvation or damnation.
At her grandmother’s request, Mari Wakatake grudgingly begins attending the Kaiho Academy. Upon her arrival, the headmaster is informed that five years ago, Mari was in an accident and lost all of her memories. As she struggles to become acclimated to her new school, she sees an alien ship.
Already disturbed by the alien ship sighting the night before, Mari is further perturbed by her obnoxious admirers. Things get even worse when Mari catches her roommate communicating with the alien ship!
Hagino is needed back on her ship, Blue, and she subsequently leaves the school. While the rest of the school is too busy worrying about a recent scandal between the faculty, Mari cannot stop thinking about Hagino. Later, a cooking session turns disastrous!
On board Blue, Hagino gives her official report to her Master Commander. The circumstances behind Mari's memory loss are revealed, which leads to her abduction!
Shibariel sends a ship to attack Blue for Hagino's defiance. Meanwhile, Akane's father is hospitalized, and Mari surprises Hagino with her efforts to help Akane see his father.
Having to work with Yuko to pass her exams, Mari discovers that Yuko is trying to uncover details about her past and lost memories. Later, they are attacked by a perpetrator sent by Shibariel.
Summer break arrives and the group spends a day at Hiroko's house. It's all fun in the sun until Hiroko's sister goes into labor, and the four friends are asked to look after her young niece!
During a visit to the dorms, Tsubael is perplexed by the decadent nature of human activities. Michiko works on a script for a play, but the stress of writer's block causes her to run away. When she returns, she finds unexpected inspiration from her friends.
Michiko's script is favorably received by her classmates. Later, after taking shelter from a storm, Mari remembers being saved on Kamioki Island and realizes it might have been the first time she met Hagino.
With the script complete, Michiko has been appointed the play’s director. Hagino, admiring Michiko’s display of openness in the play, brings Mari onto Blue for a fun ride. However, after the ship begins to have technical issues, Azaneal reveals to Mari painful details about the accident five years prior and who was to blame.
Mari, thoroughly upset by the details of the incident and Hagino’s role in it, does not want to participate in the play anymore. Hagino sits in Onomil’s quarters and cries until the specter of Onomil appears and tells her not to continue blaming herself. Azanael learns that multiple ships have been deployed to destroy Blue.
The school prepares for the festival and the play. Hagino tells about the coming Arume invasion and her hopes to protect the planet. Azanael learns that the Blue’s Emiru Force Drive’s explosion and the resulting disaster were all planned by Shibariel in order to create a new weapon. Mari’s grandmother arrives at the school for the festival, and Mari tells her that she now understands why she was sent there.
Michiko is happy that Mari and Hagino have made up and the play begins. The Arume ship closes in, but the human defense forces are no match for the new Arume weapon. As the fight escalates, the school is bombed and everyone evacuates. Hagino returns to the ship, and Mari watches from the docks as Blue heads into battle for the final confrontation with Shibariel.