The series is about the story of Kazuki Shikimori, a second year student of the prestigious magic school, Aoi Academy. Unlike ordinary people who can use magic less than a hundred times and several of his classmates, who can use magic several thousand times, Kazuki can only use his magic eight times before he turns to ash. His life changes when it is revealed that Kazuki is descended from a line of world famous magicians and he has the potential to father the most powerful magician in the world. Suddenly three girls, Yuna Miyama, Kuriko Kazetsubaki and Rin Kamishiro, enter Kazuki's life in order to obtain his valuable genes.

The story begins with a young girl named Lucy escaping under odd circumstances from an insular research facility off the coast of Kamakura in the Kanagawa Prefecture of Japan. Lucy manages to nonchalantly dismember and slay a fair number of the staff and guards with a form of seemingly supernatural power and gets outside. A sniper is seen trying to shoot her, only managing to ricochet a bullet off her metal helmet. Lucy then falls off a cliff into the sea, bleeding from her head but ultimately surviving and evading the research staff.

A diclonius' "vectors" take the form of long arms that resonate at a speed that causes them to be undetectable by sight.

Lucy is not a normal human but rather a diclonius: a mutant variant of humans with two small horns on their heads (hence the name diclonius) that resemble cat ears. The diclonius race possesses telekinetic powers through use of their "vectors", long arms that resonate at a speed that causes them to be undetectable by sight. The number and reach of the vectors depend on the diclonius.

The day after Lucy's escape, a boy named Kohta arrives at Kamakura to meet his cousin Yuka. Kohta has come to study at the local university and has been given lodging at an old, family-owned inn, the "Maple (楓, Kaede^?) Inn", provided he acts as the caretaker. After meeting with Yuka, they go for a visit to the beach and find Lucy washed up on the shore, still naked and bleeding from her head. The head trauma Lucy experienced causes her to develop a split personality. In stark contrast to the cold and sadistic Lucy, this personality is completely docile, harmless and is incapable at first of saying anything other than "Nyū". Not knowing what to do with her, Kohta and Yuka take her back to the inn to look after her and name her "Nyū". Yuka quickly decides that it will be best that she also live at the inn.

Kohta, Nyū, and Yuka begin settling into their life at the inn and Nyū begins to dredge up painful repressed memories from Kohta's past. Meanwhile, the researchers from the laboratory where Lucy was held begin searching for her, dispatching both human and diclonius agents to hunt her down.