Two years have passed since the CCG's raid on Anteiku. Although the atmosphere in Tokyo has changed drastically due to the increased influence of the CCG, ghouls continue to pose a problem as they have begun taking caution, especially the terrorist organization Aogiri Tree, who acknowledge the CCG's growing threat to their existence.
The creation of a special team, known as the Quinx Squad, may provide the CCG with the push they need to exterminate Tokyo's unwanted residents. As humans who have undergone surgery in order to make use of the special abilities of ghouls, they participate in operations to eradicate the dangerous creatures. The leader of this group, Haise Sasaki, is a half-ghoul, half-human who has been trained by famed special class investigator, Kishou Arima. However, there's more to this young man than meets the eye, as unknown memories claw at his mind, slowly reminding him of the person he used to be.
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 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.
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.
Takizawa continues his offensive against Haise on the main stage. Shirazu tries to get Saiko to help him subdue Nutcracker in the monitor room. Urie pursues Big Madam, and feels the effects of his increased Frame level.
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.
Eto drops in on a defeated Kanae, offering to help. Shirazu decides he needs to make a fresh start. Ui finally consents to Haise's idea of an undercover fact-finding mission. Haise grows frustrated probing into his past.
Matsumae and Mairo try to hold off the investigators long enough for Shu to escape. Haise and Shu face each other on the building's helipad. Quinx Squad has their hands full when a powerful ghoul stands in their way.
Eto arrives on the rooftop, spurring Kanae to attack Haise, who must also reason with Kaneki. With the other squad members on the ropes, Shirazu goes all-out to stop Noro. Kanae and Tsukiyama reach an understanding.
CCG locates Aogiri Tree's headquarters. Hinami's execution is scheduled. Takatsuki's editor is questioned over whether or not she is a ghoul. Before Takatsuki can be questioned, however, she makes a stunning public announcement.
Ayato leads a raiding party on Cochlea to rescue Hinami, He is joined by Touka and Yomo. Haise tries to get Hinami to safety, but is confronted by Furuta. As the others flee through the basement, Haise confronts Arima.
CCG's assault on Aogiri Tree on Rushima Island continues, and Urie and Saiko are anxious to rescue Mutsuki. Tatara and Kurona both make their stands against the investigators. Akira receives help from a surprise source.
As the fighting on Rushima reaches its climax, Akira makes a fateful decision. Urie, together with the new members of the Quinx Squad, continue their search for Mutsuki. Arima makes a startling revelation to Kaneki.
Kaneki assembles the remaining Aogiri Tree and Anteiku members to announce the creation of a new ghoul organization. Akira's course of treatment takes a surprise turn. Yomo and Touka both try to make peace with their past.
The CCG investigators that were close to Haise react to his leaving. Furuta takes over as the head of the CCG, and sets forth a new strategy to deal with the ghouls. The Clowns begin to riot, threatening CCG Headquarters.
Under Furuta, CCG cracks down hard on the ghoul community, forcing Goat to go underground. Takeomi and Yoriko set a wedding date. Mutsuki locates Kaneki and invites him back. Touka takes the next step with Kaneki.
Mutsuki leads the Oggais in a raid on Goat's underground lair. Urie and Kuroiwa confront Furuta in his office over his fitness to lead. Kaneki and Suzuya face each other in combat. Kaneki goes to drastic lengths to protect Touka.
As Dr. Kanou visits his family's gravesite, Kurona confronts him. CCG gains a new ally and expert on ghouls. Hide enlists the help of Akira and Amon to plead his case to CCG. A despondent Mutsuki lashes out at Saiko and Urie.
While Kaneki's body lies dormant in its giant kagune, he has an inner dialogue with Rize. Urie talks to Mutsuki about the hardships of going it alone. A crisis places the city on alert, forcing CCG and the ghouls to work together.
Following increasing dragon activity and the discovery of a second core, Kaneki and Ayato volunteer to go and deal with it. When Kaiko and the members of V launch an attack, CCG and the ghouls must fight together to stop them.
Kaneki and Furuta continue their duel below the streets of Tokyo, as CCG and Goat jointly continue fighting the members of V aboveground. Kaneki comes to terms with the events of the last several years.