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.

It’s the calm after the storm... but the calm won’t last long. Kurama and the secret facility are sending two people after Lucy. One is the newly healed and stronger Bando. The other is a diclonius just like Lucy. At Kouta’s house, Yuka and a homeless girl named Mayu talk about the events that happened two nights ago at the beach. All of a sudden, Nyuu slips and falls. She bangs her head and Lucy awakens inside of her.

After alerting the soldiers and Kurama to Lucy’s whereabouts, Nana confronts her and the two begin to fight in a cemetery. Can Nana hold Lucy off long enough for Kurama and the others to arrive? Meanwhile, hearing loud noises in the cemetery, Mayu stumbles upon the two fighting.

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...

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...

Yuka informs Mayu of Kouta's past. Meanwhile, Lucy and Mariko find each other and face off in a fight. Now, Nana and Kurama have to find Mariko because Kurama needs to kill her...