Story: 

    The story is based around the diclonius, a species of mutant humans with two cat-ear like horns and "vectors", telekinetically controlled arms which resonate at a frequency to the point in which they become transparent, and have the power to deflect or destory anything within their range. All diclonius seem to be girls only. Male diclonius are rare throughout the whole series (first one being the Professor at Kohta's school as seen in the manga), and they refer to themselves using "watashi" (私, "watashi"?), the genderless form of "I" in Japanese. They also all have pink eyes and hair unlike regular humans who have brown, black, blonde, and red hair.

At the beginning of the series, diclonii are being held for storage in a facility off the coast of Kamakura in Kanagawa, south of the city of Yokohama, held by the scientist Kurama. The first of the diclonius race, a teenage girl named by the staff as "Lucy", escapes the factory, stark naked and using her vectors to deflect gunfire and somehow effortlessly kill the security guards and Kurama's clumsy secretary in her path. However, as she makes her way out of the facility, she is shot in the back of the head by an unnamed sniper armed with a .50 calibur rifle, breaking her metal helmet and causing her to fall into the sea.

The next morning, Kouta, a university-age school student, is moving to Kamakura to study in university where he is reunited with his cousin Yuka. While reminiscing about his younger sister on a beach, who is later explained to have died "of an illness", he encounters the diclonius, still naked and badly wounded in the head from the bullet round. She is somewhat helpless and, as a result of brain damage sustained from the bullet wound, is reduced to the knowledge and capability of an infant, only capable of saying the word "Nyuu". Kouta and Yuka decide to take her with them, naming her "Nyuu" as a result.

Kouta, who is moving in to the "Maple" inn in Kamakura which was inhabited by previous generations, puts Nyuu under his care. Nyuu, still helplessly dumbfounded, has no idea of who or where she is, however Kouta and Yuka believe that they can find out where Nyuu belongs, and in the meantime, keep her safe however, Lucy and her cold character have not faded away yet; when she bumps her head, she reverts to her sadistic side, and makes transitions between her two personalities throughout the series. Kouta does not discover the real Lucy and her past inside Nyuu, however, Lucy, still with the vengeance of being rejected and abused throughout her life, begins to deliver her revenge on humans, as Kurama and the Special Assault Team continue to hunt her down.