Humanity's ultimate doomsday weapon, the Diclonius, a genetically altered homo sapien with two horns and a "sixth sense," is reported to have been hand-picked by God. Because of this frightening power, the government has taken them into custody and quarantined them in laboratories. As she makes her way out of the laboratory after killing most of the guards, Lucy, a young and crazy Diclonius, gets shot in the head. To her surprise two teenage girls named Kouta and Yuka find her on a beach. Both Kouta and Nyuu have taken her in after she lost her memory and given her the name she can only pronounce now: "Nyuu." The malevolent "Lucy," meanwhile, looks to be alive and well.