An incident involving a human-devouring Ghoul occurs in Tokyo's 13th Ward. To seek the truth behind what happened to his friend, the rebellious high school boy Taishi Fura pursues the Ghoul named Lantern with the young ace investigator Kishō Arima. The story follows how the ace investigator Arima and the talented 7th Ward investigator Taishi Fura first met.
Shuu Tsukiyama (aka Gourmet) is photographed by Chie Hori, a classmate, while eating a meal. However, she doesn't seem fazed by him or his choice of meals and is apparently in it just for photography. But Shuu Tsukiyama doubts her motives.
Amid news reports of "Ghoul" attacks nearby, ordinary college student, Ken Kaneki, encounters Rize — a girl who is an avid reader like him, at the café he frequents. Little does he realize that his fate will change overnight.
Kaneki struggles to adapt to his new nature with no success, until another ghoul, Nishiki Nishio attempts to prey on his friend Hideyoshi Nagachika and he must fight to protect him.
Yoshimura teaches Kaneki more about how to blend in with mankind, and takes in a mother and daughter needing protection. Two ghoul investigators are assigned to the 20th Ward.
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.
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.
After Kaneki and Hinami witness Ryoko's fate, the personnel at Anteiku are grieved, and Touka decides to take the investigation into her own hands. Kaneki is fed up with not being able to do anything, and decides to get 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 their own.
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 kidnapped by members of Aogiri Tree, an underground ghoul faction who is interested in his connection with Rize. Meanwhile, Amon is introduced to his new partner, the eccentric and dangerous Juuzou Suzuya.
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.
As Shinohara and Kuroiwa prepare to take on the Owl, Amon insists on joining the battle. Ayato attacks Touka, and Kaneki comes to her rescue. Meanwhile, Yomo, Tsukiyama, and Uta take on Noro, but find him to be a most unexpected opponent.
With Kaneki having left Anteiku, Touka begins studying for college to distract her from everything that is happening. Meanwhile, having incurred so many casualties while fighting Aogiri, CCG gears up to completely wipe out Aogiri Tree, as well as the Owl.
A CCG prison bus is attacked by Aogiri Tree members. At Anteiku, Touka and Hinami find out that Kaneki is involved in the attack, but each react to the news in different ways, prompting Hinami to try to be less of an imposition upon Touka.
Amon and Akira visit Cochlea in order to get information about the Owl from Amon's former foster father, Donato Porpora. However, while they are there, the facility comes under attack by a large number of Aogiri Tree ghouls, led by Kaneki and Ayato!
After living together at a CCG children's home years earlier, Kurona, Nashiro, and Suzuya are reunited in combat at Cochlea. Ayato faces an uphill battle against Shinohara, who is equipped with armor created from the remnants of his own father, Arata.
Suzuya's hellish boyhood is revisited, and it is revealed how he came to work for CCG. As Touka studies for her entrance exams, Roma, a new waitress, fills in for her at Anteiku. Tempers erupt when Akira joins Amon and Seido for supper.
Tsukiyama shows up at Anteiku with news for Yoshimura about Kaneki's attempt to become a kakuja via serial ghoul cannibalism. Concerned over her "Big Brother," Hinami accompanies Tsukiyama to a coffee shop, where she again runs into Takatsuki.
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.
Kaneki and Hide are reunited, and the two of them revisit the times they spent together. Kaneki and Touka separately remember the other members of Anteiku, as both they and CCG cope with their losses.
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.