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In 1999, Maya Kumashiro attends the funeral of her late father, the principal of Waldstein Academy when a recording left by him summons a demon that starts attacking the students, leaving her with no option but to confront it.
Maya successfully assumes her father's place as the academy's headmistress. She later meets Fumiaki Uchida whom makes his appearance from the future.
Having no luck in finding the Nostradamus Key, Bunmei meets Mikaze Nakagawa at the diner she works in. Meanwhile, people are mysteriously disappearing around the city.
Maya and Bunmei discover the cause behind the disappearences and must escape from a nest of Mothmen.
During an in-class demonstration, Kozue volunteers herself into an experiment involving Near death experience but part of herself is left in the afterlife.
Kozue's other self becomes trapped in the afterlife. To rescue her, Bunmei delves into the afterlife, although inadvertently reveals fragments of his past to everyone in the lab.
While investigating a crop circle that mysteriously appeared in the outskirts of the city, Maya discovers that it is a prank orchestrated by the Ami's father, whom wants to have Maya regain her lost passion for the occult.
Maya and Ami relationship becomes estranged since the incident with Ami's father. Before they have a chance to make up, Ami is kidnapped by a pack of chupacabra and Maya gathers all help she can in order to save her.
The spirit of a Akari, a deceased child, is accidentally summoned during a séance at the academy and Maya decides to find a way to have her finally rest in peace with the help of her friends.
Maya and her friends decide to have a Christmas party to fulfill Akari's last wish and while seeing her old house being torn down; Maya realizes the reason why her father built the Occult Academy.
Mikaze tries to convince Bunmei that Maya is actually the Key of Nostradamus and asks his to separate Maya from her spellbook, but he ends up warning Maya about Mikaze's intentions instead. After trying unsuccessfully to deceive her enemies by faking her death, Maya must escape from Mikaze whom is revealed to be a black mage.
Chihiro battles Mikaze to protect Maya but she ends up being defeated by Mikaze. With her last ounce of strength, she frees Bunmei from the spell he was put in and he rushes to help Maya defeat Mikaze.
Mikaze is defeated, but Bunmei finds that the future is still unaltered and that his encounter with his younger self is the real Nostradamus Key. When he ends up activating the key, the alien invasion begins and Bunmei regains his lost powers to stand against it by himself.