The mentally deranged Kurama, believing the clone, Cynthia, to be his resurrected daughter Mariko, grabs her from the Agent and holds her tenderly. Cynthia recognizes her genetic father, and the two embrace happily and tearfully as she finally dies from being split in half by Lucy. He howls in rage and frustration at losing Mariko once more and is taunted by the wounded Lucy, as both of them think back to how they first met.
At a time five years after the murder of Kouta's family, but just over three years before the start of the series, a young and confused Lucy is shown using her vectors to cause a woman to fatally suffer heart failure, in the essence of doing whatever her inner voice instructs her to. She wonders if this path will give her the place to live promised by it.
At the Diclonius Research Institute, Kakuzawa tells Kurama of the statistically unbelievable spike in heart failures among residents of Kamakura dwelling within a certain radius. He indicates that a Diclonius of vastly greater intelligence and cunning than most, who wildly manifest their powers around three years of age. Theorizing that it's based on the slaughter at the festival five years ago and the skill the Diclonii are using to hide out, they go on the move, concluding that this one may be the source of contagion, the original Diclonii.
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"How many years has it been since that time, I wonder?"
Remembering the horror and anger she last saw on Kouta's face as she rocks on a swing-set, Lucy, now a few years older, sees three giggling teenage girls passing by. Not knowing whether they're laughing at her or something else until they notice her, she muses that she has no place at all among humans. After being accidentally hit by a soccer ball (foot ball), she prepares to go on another rampage but is stopped by an offer of help from a young girl named Aiko Takada, who helps cover her nosebleed and takes her back to her apartment.
An always wary Lucy tries to leave after the girl has tended her wound, but she stops her and says she wants to know her. Lucy feels that this is impossible, but Aiko asks her to model for her drawings, revealing she has already sketched her in the park where she sits each day. As Lucy stands stunned, Aiko's father returns and, infuriated by her taking up drawing again instead of working, begins to beat her while chiding her to become a prostitute to provide money for the household. Lucy puts a hand on his shoulder and warns him to stop, and when he doesn't comply, she throws him up into the ceiling. She takes Aiko away as his girlfriend mocks him as well, but with Mr. Takada realizing his projection into the roof has knocked something loose and onto the floor.
In the park, Aiko reveals how she is unable to stand up to her father, and how she cannot let go of the feelings she has for her mother, who abandoned them both to become a famous artist and is currently visiting the city once more. Remembering the chance she lost with Kouta, Lucy urges her to meet with her mother and resolve the issues they have with one another, or else she'll always regret it. Aiko silently and tearfully agrees, saying she has to personally deliver the present she made her mother when she was a child. After parting ways until the next day, Lucy waits in the forest near her puppy's gravesite and reflects on what's happened. She gets a bad feeling, realizing Aiko's apartment was too small to hide something for very long properly and goes back to the apartment. In the meantime, Mrs. Takada wonders whether or not she can face her daughter after all this time.
Arriving back at the apartment, Lucy finds that the worst has happened: Aiko accidentally killed her abusive father when he tried to cut up the painting she made for her mother, her shove sending the knife into his neck instead. As Aiko despairs over whether or not she'll ever see her mother again, Lucy offers to take the blame for the killing so Aiko can meet up with her mother instead. Aiko rejects this plan, unwilling to have her friend take the blame for what she did and noting that it's her uniform covered in blood. Their plan to escape quietly fails upon the return of Mr. Takada's girlfriend, who loudly accuses the pair of murdering him. Lucy urges Aiko to come with her to meet her mother, promising she'll make it happen.
Kurama and Kakuzawa patrol the city, waiting for word of Lucy's sighting, and placing her as the murderer of four children in an orphanage, with an old photo of her, confirming her identity as a Diclonius. Word then comes that the alleged murder of Mr. Takada involves a girl matching Lucy's description.
At the mall where Aiko's mother is to have her exhibition, the pair breaks in and make their way inside, not realizing that they've tripped the silent alarms. They vow to wait, but Aiko sees a painting her mother made, one of her as a baby being cradled by her mother, overjoying her to no end. As the two wait, Lucy explains away the things she does as a magician's tricks, and she convinces a doubting Aiko by making the toys in the store all dance. Aiko bear-hugs her and makes plans for activities the two will do together.
Kurama and Kakuzawa turn on bright lights, trying to confirm if one or both girls are Diclonii. Lucy throws objects, displays, and even pieces of the floor itself at the attacking soldiers. In the chaos, Kurama manages to come about at the children from the rear and shoots at her but hitting Aiko, who jumped in the way to protect her friend. Lucy, in shock at Aiko's sacrifice, screams out in rage, and her vectors tear an enormous hole through the ceiling. Outside, Aiko's mother watches in the distance on the street with the other evacuees, never knowing how close she came to seeing her daughter once again.
As the attack force regroups, Lucy vows to keep her friend alive. Confronted by a cold-hearted Kurama, who regards Aiko as just another killer, she agrees to surrender in exchange for getting her friend medical help, that ultimately fails to save her. His words continue to be harsh as Lucy enters custody, and again later, when she is secured at the island facility when he blames her death on them not immediately surrendering and on the refusal of the Diclonii to co-exist with humans. For his bitter words and most of all for his failure to keep his word and save Aiko, she vows to kill everyone he cares for while leaving him alive to suffer the same loss over and over.
In the present, still in agony over losing her horn, Lucy screams anew at Kurama, asking how it feels to lose someone, at which Kurama finally runs off with Cynthia's remains. The Agent shoots off Lucy's other horn, then calls for pickup, exasperated at a very long day and a complicated mission.
At the nearby hospital, Kouta is still unconscious, but his condition is not as severe as was feared. Yuka's mother offers her home to stay in but is upset with the situation, both the status of Maple House and the injuries and questions why Nyu was allowed ever to stay there, which Yuka defends halfheartedly in the face of all that has happened.
Mayu reports on Nozomi, who can still barely speak due to her throat injury. The doctors are unsure at that time exactly how and when to treat her, which Yuka calls for a cruel thing to happen just as Nozomi passed her exams. Mayu observes Nana dressed in odd clothing and keeping to herself while explaining that her wounds heal quicker than the others because she is different. Nana leaves to go to the toilet, and unable to find it, overhears an argument between Yuka and her mother, who worries that Nana could become a murderer just as Nyu did, without warning. In the toilet, Nana again fears there will never be a place for her, but resolves to be strong. Putting on a happy enthusiastic face once being reunited with the others, offering to help in any way she can. Not wishing to leave the side of her injured friends, especially Nozomi, Mayu asks Nana to deliver onigiri to the homeless man living on the beach she has been attending to. With an enthusiastic front that concerns the others, Nana agrees to do it, hiding her tears as she goes.
Elsewhere in the hospital, Nousou and Barbara had both survived the helicopter falling on them, while Nousou mourns the loss of Alicia and Cynthia, and wondering openly about their controls, as well as being mocked gently by the Agent, who pulled them both from the flaming wreckage.
A homesick Lucy/Nyu is revealed to have been brought back to the underground grotto, and held nude and bound by Chief Kakuzawa, who brags that the hour for the Lebensborn Project to begin is finally at hand, with Lucy bearing the children of the new race.
At the beachfront, Nana is shocked to find that the homeless man Mayu has been attending to is, in fact, her 'papa', Kurama, who is still cradling Cynthia's upper torso and calling it Mariko. He violently rejects her aid and presence, harshly dismissing her as having been nothing but a test subject.