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!

Kaneki desperately fights the urge to eat human flesh, the only thing that can satisfy his hunger as a ghoul. He meets up with Hide again, joining him on an errand, and is glad for the companionship. But will his declining condition place Hide at risk?

Yoshimura teaches Kaneki more about how to blend in with mankind, and takes in a mother and daughter needing protection. Two ghoul investigators, Mado and Amon, are assigned to the 20th Ward. In response, Toka takes Kaneki out to have a mask made for him.

Kaneki starts receiving self-defense lessons from Yomo. He meets Itori, who runs her own bar, and is friends with Uta and Yomo. Kaneki is befriended by Tsukiyama, a ghoul who knew Rize, who also enjoys reading, and possesses other, more epicurean tastes.

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.

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.

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.

The 11th Ward offices of CCG are attacked by ghouls, wiping everyone out. Banjo and company stop in at Anteiku, looking for Rize to warn her to flee from Aogiri Tree, a new group of ghouls bent on taking over-- until Kaneki accidentally knocks him out!

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.

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.

Kaneki and Ayato rescue Naki, one of Jason's old cohorts from CCG custody, and prepare to storm the maximum security prison for Ghouls known as "Cochlea". Meanwhile, Tōka pays a visit to the university were Kaneki used to attend, where she has an encounter with Hideyoshi.

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.

The battle at Cochlea intensifies on several fronts and when Ayato is to be almost killed, he is rescued in the nick of time by Kaneki, who undergoes a bizarre transformation after consuming the bodies of several dead Ghouls to empower himself.

The appearance of the "One-Eyed-Ghoul", considered the most dangerous of them all, leaves the CCG in a state of alert while Kaneki writhes in pain due to his new condition.

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.

During Kaneki's visit with Yoshimura, he asks for information about the Owl, and is told the tragic tale of a young ghoul named Kuzen. Touka makes plans to move out of Anteiku. A snowy day brings with it brisk business at the coffee shop.

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.

The battle between CCG and Anteiku continues, and Koma, Irimi, and Yoshimura each engage the special investigators. When a civilian gets caught in the middle, Hachikawa continues to press his attack unabated. Shinohara receives some unexpected advice.

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."