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 members of Quinx Squad, an experimental division of Akira Mado's CCG squad, and composed of investigators who have been surgically made part ghoul, work to track down the A-rated ghoul Torso.

Haise loses control while fighting Orochi, and has to be subdued. Later at the Chateau, Haise berates Urie for not getting the squad to safety, and removes him from his squad captaincy. Urie seeks to increase his power.

Urie speaks to Chief Washu about having his Frame level increased. With a mission coming up, the Quinxes try to get Saiko to come to work. Donato asks Haise about his missing memories. The squad goes undercover.

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.

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.

The Clowns act as auctioneers for a human auction, in which Mutsuki finds himself embroiled. CCG forces surround the complex in which the auction is being held, with orders to exterminate the ghouls inside--especially Big Madam.

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.

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

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.

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."

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.

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.

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.

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 Quinx Squad rushes to save Mutsuki from Kanae. The Owl goes on a seemingly unstoppable rampage. Urie is frustrated when he is assigned escort duty. Ato Squad meets resistance trying to secure the monitor room.

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.

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 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?

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.

Haise asks Arima to allow him to take custody of Hinami, and the remaining ghouls retreat. Following an awards ceremony where many of the investigators are promoted, Haise hosts a celebratory dinner at the Chateau.

Tsukiyama's condition worsens. Tatara and Ayato argue about rescuing Hinami. Shirazu finds it difficult to take possession of the Nutcracker quinque. Quinx Squad begins a new joint investigation with S1 Squad.

Having seen a photo of Haise, Tsukiyama bounces back and races to see him. Haise takes the rest of the squad to Uta's shop to be fitted for masks. Kijima releases a shocking video on the CCG website to draw Rose out.