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 destroy anything within their range. Most diclonius seem to be girls; male diclonii 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?), the genderless form of “I” in Japanese. In the anime they also all have pink eyes and hair unlike regular humans who have brown, black, blonde, and red hair. In the manga, their hair coloring can be as diverse as a normal human’s (ex. Nana and Mariko have purple and blonde hair, respectively, in the manga).
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, effortlessly kills 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 caliber rifle, breaking her metal helmet and causing her to fall into the sea.
The next morning, Kohta, a university-age school student, is moving to Kamakura to study in a 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 “Nyu”. Kohta and Yuka decide to take her with them, naming her “Nyu” as a result.
However, Lucy and her cold characteristics have not yet faded away; when she bumps her head, she reverts to her sadistic side, and makes transitions between her two personalities throughout the series. Yuka, who is in love with Kohta, begins to envy the attention he gives to Nyu, remembering their relationship together as children, however Kohta is still anxious about finding out who Nyu really is.
Kohta, who is moving into the Kaede House (which was a traditional Japanese restaurant that was inhabited by previous generations) in Kamukura, puts Nyu under his care. Nyu, still helplessly dumbfounded, has no idea of who or where she is, however Kohta and Yuka believe that they can find out where Nyu belongs, and in the meantime, keep her safe. However, after Kohta gets angry at Nyu, she runs off back to the beach where she was found. The homeless girl Mayu and her dog encounter Nyu, and Kohta traces Nyu back to the beach, discovering that Kurama has organized a Special Assault Team, led by Bando, a ruthless, cold-hearted soldier, and Nana, another Diclonius, to hunt her down. However, both of them are no match for Lucy, having their limbs ripped off by Lucy’s vectors. Eventually, Kurama decides to take them back to Kamakura, Bando to find Lucy, and Nana to be released into the world contrary to the instructions given to Kurama to put her down.
Mayu and Nana both end up living in Kohta’s household, where significant parts of their past come together. Kurama, having released Nana and Bando already and still failing to capture Lucy, resort to his last weapon – his daughter Mariko, a powerful diclonius known as “#35″, as a final attempt to dispose of Lucy, at the risk that she also create the same destruction on humans as her.
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