The mini-series follows 16-year-old Aika Sumeragi, who recently got her C-class license to be a salvager, a person who searches for treasure among the ruins of the Earth’s cities which have been submerged following worldwide earthquakes. However, at high school, she is regularly late for class and then her posters advertising her salvaging services are taken down. However, one afternoon, she is invited by Eri Shinkai, the class president, to join her Treasure Hunting Club where they look for the coordinates hidden away in a tattoo on classmate Karen Minamino. Aika gladly accepts, but during the trip some of her schoolmates and even their club advisor attack them in an effort to try to capture Karen. Aika defeats the girls and discovers they are being controlled by some devices implanated on their body. As they approach the destination, Karen starts acting strangely as if she remembers being there before. At the underwater base, Aika, Eri, and Karen make their way to a locked lab, and discover Karen’s true identity.
In Aika Zero, 19-year-old Aika Sumeragi is called to investigate the goings on at a private Catholic school that is run by a council group called the White Knights. Aika, Eri, and Karen discover that the White Knights. In the school, the students have been mysteriously disappearing and those who have returned have no memory of the event. They discover that there are aliens who use rope-like tendrils to probe the girls, knocking them out and harvesting their energy, or possessing them to do their bidding.