Suddenly Ayato is surprised to see his mother and two of her Dolems attack. Ayato leaves Tokyo Jupiter, and one of the Dolems kills Ayato's mother, Mishima. Ayato, kills the Dolems and leaves Tokyo Jupiter. Meanwhile, Haruka joins an organization called Terra.

Kunugi takes the day off. Quon visits him and plays some music for him, but its incomplete. She goes a little crazy because the song doesn't have an end. Meanwhile, Kunugi goes on a ship for a birthday date, talking to his former wife. She says that he didn't spend enough time with his daughter, using work as an excuse. She gives him the last part of the music. His daughter wrote the music for him. It's her birthday, but she's dead. He visits her grave. Quon finishes the song.

Itsuki, Helena and Isshiki grew up together as students of the Bohbem Foundation. While many of the other students exhibited special abilities, Isshiki showed little talent and was considered to be normal. When Isshiki finds a stone-like creature, his desire to protect it awakens something within him that he never realized he had.

All that Ayato has known about his life proves to be a lie: his mother is not who he thought she was, his old friends are spies and Tokyo Jupiter is infested with Mu. The only person he can trust is his old school friend, Hiroko Asahina. Together they decide to escape the city for the real world

Ishiki plans to destroy the barrier around Tokyo Jupiter. Souichi is planning on tricking him somehow.

Ayato finds out from Itsuki that Haruka is in love with him, and is hurt that he didn't even know and he's been avoiding her.

Mamoru has been going through Ayato's stuff and has found out that he's close to Megu by listening to his cell phone message. He spends more time with her. He also finds Hiroko's diary, with the blue blood and the good-bye message. Later, he walks outside with Megumi. Ayato finds them. Mamoru grabs Megu around the neck and says that Ayato killed Hiroko, even though he knew she loved him. He says that Ayato will have to make a choice soon, and he will no longer be human. He punches Megu in the face.