Please Note: These arc titles are not official and do not appear in-story. These are compressed digest overviews of major events from the series. More detailed chapter entries are also available.
Time has passed since Mayu came to live at the Maple House, and while Kouta and Yuka have concerns about Mayu's mother and living expenses, they are both happy to see Mayu happy. As the two attend university together, things become awkward both because of their relationship and because they must take the childlike Nyu with them. Once there, Nyu has several encounters both comic and otherwise, including one with Bando that again ends badly for the wounded soldier.
Professor Kakuzawa gives Bando a harsh choice, but he ultimately refuses and rejects the scientist's offer, believing it to be insane and delusional. Bando also manages to evade efforts to castrate him for pursuing a one-man campaign against Lucy, once he is outfitted with bionic replacements for his lost limb and eyes. He also again encounters Mayu, who he suspects knows something about Lucy, and a bond that Bando resists begins to form between the two.
Back at the Diclonius Research Institute, Nana and Kurama bond as best they can in light of her injuries and rehab with new artificial limbs, and plan for their imminent departure. This is made more paramount by Chief Kakuzawa's eventual order to execute Nana.
Some of Nyu's home antics cause Mayu to begin to mistrust Kouta.
Kouta and Yuka's efforts to keep Nyu from drawing attention fail at the worst time when they are in the class of Professor Kakuzawa, who recognizes Nyu as Lucy. With a mix of lies and threats, Kakuzawa tricks them into leaving Nyu in his care. Kakuzawa plans to displace his father, Chief Kakuzawa, by raping and impregnating Nyu, but his efforts only succeed in bringing out Lucy. Revealing that he is also a Diclonius, he makes an offer of alliance with Lucy to repopulate the Earth with their kind, which she rejects by killing him.
At the Maple House, questions arise as to the legitimacy of the Professor's claims. Going alone despite tensions with Yuka, Kouta meets Arakawa, the Professor's assistant when goes back to the University, and both discover the severed head of the Professor. At Arakawa's urging, Kouta leaves quickly, still wondering where Nyu is, and hearing dire warnings about the savage nature of horned people. Arakawa decides to contact the Professor's family regarding his death, which Chief Kakuzawa seems to dismiss without any reaction, even extending threats to those Kurama regards as family.
As Kouta and Yuka search for the once-again lost Nyu, the two grow closer on an emotional and physical level.