Lucy is a unique human subspecies known as a Diclonius, born with small horns and invisible telekinetic limbs that make her a target for cruel government experiments. When she gets the chance to flee, Lucy, hardened by her imprisonment and torture, unleashes a wave of violence to escape her captors. During her escape, she suffers a severe head wound that causes a split personality: a persona with the mind of an innocent child and limited speech. In this unstable condition, she encounters two college students, Kouta and his cousin Yuka, who unknowingly take in an injured fugitive, unaware of her violent nature. This act of kindness will alter their lives, as they are soon pulled into the dark world of government secrets and conspiracies.