The Diclonius, a mutated homo sapien that is said to be selected by God and will eventually become the destruction of mankind, possesses two horns in their heads, and has a "sixth sense" which gives it telekinetic abilities. A diclonius' "vectors" take the form of long translucent or invisible arms. Due to this dangerous power, they have been captured and isolated in laboratories by the government. Lucy, a young and psychotic Diclonius, manages to break free of her confines and brutally murder most of the guards in the laboratory, only to get shot in the head as she makes her escape. Which causes her a memory failure. n 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".
 
She survives and manages to drift along to a beach, where two teenagers named Kouta and Yuka discovers her. Having lost her memories, she was named after the only thing that she can now say, "Nyuu,". 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 "dead".