The fight against Tsukiyama is resolved, but Touka wants to kill Kimi, now that it's clear she knows that Nishiki and Kaneki are ghouls. Meanwhile, Hinami is eager to see her father again after being apart for so long, and acts out when she is unable.

After Kaneki and Hinami witness Ryoko's fate, the personnel at Anteiku are grieved, and Touka decides to take matters with the investigators into her own hands. Kaneki is fed up with not being able to do anything, and makes up his mind to become involved.

Touka sets out to lure the ghoul investigators, but before she can strike, she finds that Hinami has run away. When Touka and Kaneki go out looking for her, they find themselves face to face with Amon and Mado, who has a few surprises of his own for them.

Kaneki is held captive by Yamori, who practices his torturous craft on him. The police and CCG move in to deal with Aogiri Tree, who have made an 11th Ward shopping mall their headquarters. In all the commotion, the Anteiku team tries to rescue Kaneki.

As Yamori continues to brutally torture Kaneki, Rize once again appears to him, and the two of them explore Kaneki's childhood and relationship with his mother. Kaneki is forced to make a choice that has a profound impact on him.

Having defeated Jason and accepted his ghoul half, Kaneki joins Aogiri Tree to protect those close to him in Anteiku.

Aogiri commences their invasion of Cochlea and free a majority of the imprisoned ghouls while Amon and Akira visit the prison to learn more about Aogiri's plan from Donato Porpora. Amid the battles between the CCG, Cochlea security and ghouls, Kaneki meets a ghoul named Orca with orders to break him free, but is attacked by him instead.

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.

Yoshitoki is granted permission to execute the operation to eradicate the Owl. The many CCG officers involved in the mission take time beforehand to write any last words they might have, as the 20th Ward is cordoned off and its civilians evacuated.

Suzuya is left to face the newly-arrived one-eyed Owl on his own. Aogiri Tree joins the battle against CCG, who find themselves overwhelmed by the sheer number of opponents. Meanwhile, Kaneki confronts Amon, who stands in his way to Anteiku.

After waking up in Anteiku, he hears someone mention that "making coffee is difficult." When the person comes out, it is revealed to be Hide. By the time that Kaneki realises that he has his ghoul eye activated, Hide tells him "I Knew."