As Shinohara and Kuroiwa prepare to take on the Owl, Amon insists on joining the battle. Ayato attacks Touka, and Kaneki comes to her rescue. Meanwhile, Yomo, Tsukiyama, and Uta take on Noro, but find him to be a most unexpected opponent.
Now with Kaneki at their ranks, the Aogiri Tree takes the offensive against the CCG, and Amon is introduced to Mado's daughter Akira, who is assigned to become his new partner.
A CCG prison bus is attacked by Aogiri Tree members. At Anteiku, Touka and Hinami find out that Kaneki is involved in the attack, but each react to the news in different ways, prompting Hinami to try to be less of an imposition upon Touka.
Amon and Akira visit Cochlea in order to get information about the Owl from Amon's former foster father, Donato Porpora. However, while they are there, the facility comes under attack by a large number of Aogiri Tree ghouls, led by Kaneki and Ayato!
After living together at a CCG children's home years earlier, Kurona, Nashiro, and Suzuya are reunited in combat at Cochlea. Ayato faces an uphill battle against Shinohara, who is equipped with armor created from the remnants of his own father, Arata.
Suzuya's hellish boyhood is revisited, and it is revealed how he came to work for CCG. As Touka studies for her entrance exams, Roma, a new waitress, fills in for her at Anteiku. Tempers erupt when Akira joins Amon and Seido for supper.
Worried about Kaneki's disappearance, Hinami wants to do something for him, but is uncertain about it, until Kaneki appears at Anteiku and she calls for Touka to see him again.
The CCG launches a full scale attack on Anteiku and instead of running away, Yoshimura and his friends decide to make a stand against them, and despite being warned, Touka and Kaneki depart to the 20th ward to assist their friends as well.
Kaneki's friends from Anteiku are being defeated one by one but he arrives in the nick of time to save them. Meanwhile, Juuzou, Shinohara and a few other investigators corner and defeat Yoshimura after a long battle, but suddenly, an even greater threat appears before them.
When the Aogiri Tree joins the battle, the CCG is driven into a corner until their strongest investigator, Kishou Arima appears to assist them. Meanwhile, Kaneki and Amon face off.
Kaneki and Hide are reunited, and the two of them revisit the times they spent together. Kaneki and Touka separately remember the other members of Antieku as they both and the CCG cope with their losses.