At the Diclonius Research Institute, Chief Kakuzawa lightly mocks the obvious discomfort of Arakawa as they walk through the underground lair, which he calls both the Eden and the graveyard of his relatives, including his son, with each standing stone being a grave marker. He asserts that Lucy will be the genetic ancestor of the species that replaces homo sapiens (humans), just as the mitochondrial fossil, Lucy, was to humankind, rendering the man who controls Lucy as the Father and God of the new race. Arakawa calls out some of the details of his plan, saying it took two-hundred thousand years for the humans to predominate, and that, despite rapid growth in the Diclonius population, such a replacement will still take thousands of years. Kakuzawa stuns her by saying this replacement will begin within one year.
At the Kamakura beachfront, Nana begs Kurama to deny that Mariko is his real daughter. Mariko asks to know the details of her life, including what happened to her mother and if he tried to kill her when she was born. Kurama tells her yes, and asserts that he killed his wife as well, despite Nana's denial of this being true. As Mariko breaks down in tears asking why all this is true, Kurama begins to describe his recruitment into the employ of the Kakuzawas and their agenda.
The narrative shifts to the past, when he, as a young graduate student, meets and debates with his sometime friend, the future Professor Kakuzawa, who challenges him with ideas about mitochondrial origin theory and a new project his father heads, a cutting-edge facility researching the secrets of human evolution. Kurama accepts this offer for its promise of vast funding and few limits on the terms of the studies, but when he arrives at the facility, he immediately begins to think of it as haunted and worries about his choice.