An unknown girl with invisible hands, or vectors, and telepathic powers escapes from a secret facility. The next day two cousins, Kouta and Yuka, find her. But she is different from before. She can only say one word, nyuu. Not knowing anything about her, the two cousins take her in. Kurama, the head scientist from th efacility where she escaped, has sent a merciless man, Bando, after her.

Bando escapes from the hospital, still trying to find Lucy to satisfy his grudge against her. Professor Kakuzawa Yū's decapitated body is found by his assistant and Kohta. While searching for Lucy, Kohta and Yuka develop a fondness for each other as displayed through a kiss. Finally, Lucy is found by Kohta and Yuka and taken back home.

After Lucy is knocked out by Nana Kouta tends to her. She sleeps and relives her childhood in a dream, revealing many things about her. Meanwhile, Nana tells Mayu about Lucy and the diclonius and Arakawa is called in to work for Director Kakuzawa...

More of Lucy's past is revealed: Her meeting with Kouta, their friendship that will end in tragedy, and the reason why Lucy became the killer she is today.

Number 35, Mariko, is released and immediately kills the soldiers around her. The professors, who were prepared for this, set off one of the explosives inside her, destroying her arm. Later, they fly her to where Nyuu and Nana are. Meanwhile, Nana is enjoying living in the inn but Kouta tells her she needs to work as well. Things seem to be going as peaceful as it can get...