Kouta and Yuka finally become closer and begin to repair their past wounds.
In a small fragment of the underground grotto that survived the sinking of the island, Anna Kakuzawa emerges alive and well, her monstrous oracle form having been a shell her father crafted to make her a living computer. Anna hears a sound and covers her post-emergence nudity at someone's approach. It is the Agent, who is also alive, having had the attacking Clone Diclonii washed away by the flooding, wandering for days on end---and revealed to be a woman. She and Anna argue lightly until the Agent asks Anna how they can get out of there. Anna at first believes she knows but then realizes that her knowledge as a living computer is gone now, much to her relief. Thrown off by the young girl's behavior, the Agent makes the practical but repulsive suggestion that they eat the monster shell of Anna's oracle form.
At Maple House, Mayu wonders where Wanta is. The small dog has wandered outside, and passes Nana at a series of grave markers, saying how she is not lonely despite her papa not being there, since she has all her friends. We are led to believe it is Kurama who died, but in fact, he is right behind Nana and is merely going to the cemetery to give a proper burial to Mariko's ashes. They are finally living together (whether this is in their home or if Kurama is staying at the Maple House is never made clear), and Kurama promises that they will be together once he cleans up some loose ends from the situation that has dominated their lives. Nana begs him to become his wife and make babies with him. As he begins to answer her with what it looks like to be a dismissal of her request, Wanta leaves them without hearing the rest of his reply.
Wanta then passes by a flyer for an art gallery featuring an artist named "Aiko Takada" and comes upon Mayu, who is still cleaning up the beach months after Bando's supposed death, and wondering where her dog has gone. While she is proud of her efforts, she amusedly imagines that Bando would not praise her for it, only to hear her imitation of his words from Bando himself, apparently with even more plastic parts than before, telling her again that he could never die. Lovingly and overwhelmed with joy, Mayu flings her arms around Bando and begins to cry in happiness as Wanta turns and heads for home.
The last day of the summer festival arrives, with Nozomi and Yuka dealing with the heat, and Mayu putting up with Nana mocking her for being so hungry, she eats cotton--not understanding about cotton candy. Kouta excuses himself to Yuka and leaves them, saying he must visit an old friend.
When he gets to the promised spot Lucy/Nyu spoke of, he realizes she won't be there, and begins to think that maybe that promise was meant for next year. For the next ten years on that same day, he returns and waits for her to keep her promise to be waiting there for him.
That tenth year, he arrives in the company of a little girl who greatly resembles a young Yuka. She is Kouta's daughter Nyuu, to whom he explains the reason he comes there, and that he used to play with his friend there when they were children. Nyuu explains that she plays there too, with a set of twins who are her friends, arguing the obvious point with Kouta when he says she shouldn't play there. They stay for a time, but when her papa's friend doesn't come, Nyuu suggests they get back before her Mama (the child genuinely resembles young Yuka, though her mother is never named) is angry at them for being too late. Looking over by the stone that marks the first Nyu's puppy's grave, the little girl notes a jar that has surfaced. It contains the jade stone Kouta once gave her as a gift, and a letter that gives thanks to him for the stone, confesses her desire to marry him and reveals her real name - Kaede - at long last. Knowing for certain that their early friendship and love was genuine and that her heart was human, after all, Kouta cries tears of joy for having found his real friend at last.
Little Nyuu then sees her two friends approach them, one of whom is named Kaede. The twin girls tell Kouta that they have been waiting to meet someone there, their very special and important friend. We see them only partially, and it is impossible to tell if they are humans or Diclonii, but it is apparent from the look of joy on Kouta's face that they Lucy and Nyu, are possibly the reincarnations of Lucy and Nyu.