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.

The offshore facility, headed by the scientist Kurama, sends a special task force, headed by the ruthless, cold-hearted assassin Bando, to hunt down Lucy at a beach in Kamakura. However, they only encounter her in her innocent "Nyu" state. She is hit over the head by Bando. Bando then tells his partner to finish Nyu off, but the hit reverts Nyu back to Lucy, who kills Bando's partner, and goes after Bando. Lucy uses a firearm to shoot and injure Bando. In the end, Bando has been dismembered and blinded. Lucy reverts to Nyu before she is able to kill Bando. It is seen here that Lucy and Nyu switch between each other depending on the events surrounding them. After being injured by Bando, Kohta is put in the hospital, but is not severely injured, and is released hours later while Yuka goes looking for Lucy. He encounters her back at the house and forgives 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.

Mayu’s tragic past is revealed. She remembers back to when she ran away from home. At school, Yuka and Kouta’s new professor is none other than Yu Kakuzawa, Chief Kakuzawa’s son. He instantly notices Nyuu as Lucy and tricks Kouta into handing her over to him.

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 fighting, Bando and Nana realize that they are allies and not enemies. Nana agrees to bring Lucy to the beach when she senses her. Meanwhile, at the temple, Mayu meets Nana. The two become friends and Mayu agrees to bring Nana back to her house for food.