Kouta and his cousin Yuka have no idea whom they are helping when they take an injured young woman into their care. To the two college students, she appears harmless, with a child's mentality and little ability to speak. She is actually Lucy, a fugitive whose escape from government captivity has left a trail of bloodshed.
Lucy is a Diclonius, a type of human born with small horns and invisible telekinetic hands. Subjected to inhumane government experiments, confinement and torture, she turned violently on her captors when an opportunity to escape arose. A severe head injury during the breakout left her with a split personality, giving rise to the childlike state in which Kouta and Yuka find her. Unaware of her murderous tendencies, the cousins become entangled in the government's secrets and conspiracies.