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.

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.

Lucy and Nana start to fight, but Mayu stops them and Lucy turns back to Nyuu, hugging Kouta and telling him she likes him. Later, Kurama's past is revealed and so is more about the dicloniuses.

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...

Mariko is torturing and playing with Nana like an insect while Kouta runs to her to protect her. Mariko temporally looses her vectors, thanks to Nana, and has to be sent back. Nyuu follows Kouta, but when the soldiers start to shoot at her she turns into Lucy. Seeing the bloodthirsty Lucy, Kouta recalls everything...

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...