Rakka goes to work with Nemu at the library. There she meets Sumika, a kindly pregnant woman who is interested in Rakka's perspective as a newborn. Nemu tells Rakka about an old, unreadable book called The Beginning of the World. Rakka learns about another group of Haibane, both male and female, living in Abandoned Factory on the other side of town.

Rakka refuses to believe Kuu will never return from her Day of Flight, and sickly black spots begin to appear on her own wings. Depressed, she goes to town alone and is approached by Hyouko, a Haibane from Abandoned Factory who asks about Reki. Reki gives Rakka medicine for her wings and tells her about the Sin-Bound Haibane and about her own past.

A flashback shows the kindly Kuramori, who promised to stay with Reki forever. In the present, Reki goes to the Haibane Renmei to ask for help for the ailing Rakka, and is told that Rakka is no longer Sin-Bound. Rakka is given her own job within the wall around the city, and the Haibane from Abandoned Factory offer a tentatively friendly gesture.

Midori, from Abandoned Factory, gives more hints about Reki's past. The Communicator tells Rakka that while she had the birds to offer her forgiveness, Reki will not accept anyone's help, and has little time left. Rakka vows to try and help her. Visiting the library, she talks to Sumika about an old book. Resigned, Reki works on a secret painting.

The Haibane go into town to buy Bell Nuts, gifts of reconciliation for the Passing of the Year festival. Reki gives one to Hyouko, and he and Midori finally tell Rakka what happened. Rakka learns about the Renmei's sign language, and the Communicator gives her her true name. After the festival, the Haibane of Abandoned Factory send Reki a message.

Rakka discovers that Reki's entire studio is painted like her cocoon dream. She gives Reki a box from the Communicator, containing her true name, which fills Reki with despair. She throws Rakka out of the room, confronts a manifestation of herself, and relives her dream. Rakka realizes the truth about Reki's struggle and goes back to save her.