Amid news reports of "Ghoul" attacks nearby, Ken Kaneki points out Rize, a girl he is interested in, to his friend Hide at a local coffee shop. When Kaneki discovers the two share a favorite author, he asks her out. However, their date ends in tragedy!

When Touka falls ill, Kaneki pays her a visit that has unexpected consequences. Meanwhile, as Nishiki is still recovering from his run-in with Kaneki, he is nearly preyed upon by other ghouls. Tsukiyama remains consumed with the idea of having Kaneki.

After several weeks go by, everyone tries to return to their normal lives. Hinami moves in with Touka, and despite her aversion to birds, they nurse an injured cockatiel they name Hetare back to health. Kaneki visits Itori to try to learn more about Rize.

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.

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."