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Lucy escapes from the facility where she has been contained after killing much of the staff. A sniper shoots her in the back of the head as she is escaping and she falls off a cliff into the water below. Kohta and Yuka find Lucy and try to help her, but she cannot remember anything, nor understand the language. They take her home and call her “Nyu” because that is the only word she can say. Meanwhile, a Special Assault Team is after Lucy with orders to kill her.
Police comb the city trying to find Lucy's location. Kohta finds Nyu at the beach where Bandoh, a member of the SAT and his partner are scouting. Nyu is discovered by the team and becomes Lucy. Meanwhile, Yuka finds Kohta and takes him to the hospital. When he gets home, Nyu is waiting for him.
Nana, a Diclonius, has accepted the request to find Lucy. Kohta catches a cold and Yuka, who came to bring clothes for Nyu, realizes something is wrong. Nyu hits her head and becomes Lucy, but after having a flashback of Kohta, leaves. While Lucy is gone, Nana finds her and tells her she will take Lucy back.
Lucy and Nana fight, and Lucy is wounded. Lucy transforms back into Nyu and meets Yuka by accident. Yuka finds out that Mayu may be homeless. Meanwhile, Nana returns to the facility and Kurama's boss insists that Nana must die because she is now useless.
During the night with Kohta and Yuka, Mayu leaves the house, leaving a note that suggests she didn't want to be a burden on them. Kohta and Nyu show up just in time to tell the police that Mayu is a family member. Kohta and Yuka take Nyu to their school and Professor Kakuzawa, who is a Diclonius, notices it is Lucy.
Kohta returns to school and tries to talk to the professor, but only finds the assistant in his office. She takes him to find the professor dead in the basement lab. The following morning, Kohta and Yuka go to look for Nyu. They find Lucy in a shrine and tell her that the Kaede House is her home. Bandoh, recovering from his injuries, escapes from the facility and goes on a hunt for Lucy. Meanwhile, Nana arrives on the shore.
Nana suggests to Bandoh that they work together since their goal is the same—to find Lucy. He rejects her offer, but tells her to make contact with him once she finds her.
Nyu loses consciousness when Nana knocks her out. Kohta then slaps Nana and she tries to tell them that Lucy is a very bad person. Meanwhile, Lucy surfaces but comes down with a fever. While she is sleeping, she has a dream about her childhood, how she came to use her vectors, and how she came to mistrust humans.
Lucy dreams about her childhood. She killed many people at the children's home because some boys killed her dog friend.
When Nana and Lucy meet, Nana tries to fight again. Elsewhere, Director Kakuzawa gives and order to use #35, whom is said to be a worse monster than Lucy...
A cleaning contest between Nyu and Nana end with an accident that knocks Nyu unconscious. When she, now Lucy, awakens, she remembers the day she met Kohta...
#35 has been released. Kurama leaves the facility to talk to Bandoh; they make a deal that involves the destruction of Mariko. At the Kaede House, Nana hopes that Nyu doesn't transform to Lucy so they don't have to fight.
When the order is given to kill Nyu, she reverts back to Lucy and uses her vectors to repel bullets, thereby saving Kohta. This action unlocks the memory of Kohta's sister and father and how they were murdered.