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In the future — in a world mostly submerged under water — the 19-year-old Sumeragi Aika goes to college while training as an agent by assisting in Aida Gozo's salvaging business.
19-year-old Aika reunites with Eri and Karen to investigate the serial disappearances of school girls at St. Aero academy. Some of the girls have returned but without any memories of what has happened. While going undercover as students, they discover that the student council group called the White Knights have been abducting the students, and that they are in cahoots with an alien force that penetrates and captures the girls using rope-like tendrils of light. Aika is captured by the alien, but is rescued by Risako.
Miyu's back story is expanded upon regarding how she encountered the aliens and then influences her classmates to join her in the student council. The army takes over responsibility for the investigation. When Karen goes in undercover, she notices the council has deserted the chapel. Meanwhile, the Hagens have been observing their actions. When the White Knights capture more girls, Aika raids the underground.
E.T.A.I. holds Aika captive and attempts to probe her, but the tendrils are broken by Aika's inherent power. E.T.A.I. and Miyu go to the spaceship where E.T.A.I. reveals that Aika has alien powers like her. After Aika defeats Rin and Kana, she reunites with Karen and Risako and they find the captured girls. Aika defeats Miyu and E.T.A.I. and then goes after the spaceship where, with the help of the military, they shoot it down. Aika returns safely. During the closing credits, Miyu and E.T.A.I. are taken in by the Hagens.
