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.

Shuu Tsukiyama is a ghoul: a creature who eats human flesh, and he likes to enjoy his meals to the fullest. One night, while relishing in the premeditated murder of his dinner, Shuu's much anticipated first bite is disturbed by a sudden flash of light. The flash turns out to be from the camera of high schooler Chie Hori, who presents Shuu with the perfect picture capturing his true nature; the extremely clear shot of a bloody corpse and an overly excited Shuu threatens to expose his ghoul identity, thus Shuu needs to sort out this situation quickly. After Shuu discovers that Chie attends the same high school as him and is even in the same class, the reason behind his feelings of obsession changes from self-preservation to morbid curiosity. As he grows closer to the absent-minded and extremely odd photographer, he challenges them both to learn more about each other's conflicting worlds; Shuu promises that Chie will come out of this experience with a photograph superior to the one she already has.

After the conclusion of the Tsukiyama Family Extermination Operation, the members of the Commission of Counter Ghouls (CCG) have grown exponentially in power and continue to pursue their goal of exterminating every ghoul in Japan. Having resigned from Quinx Squad, the now seemingly emotionless Haise Sasaki begins taking on more and more tasks from the CCG with no regard to the difficulty. Despite his vacant expressions, Ken Kaneki's memories are resurfacing in Haise, leaving him in a state of internal conflict. Meanwhile, his new coldhearted behavior is affecting the people around him. Quinx Squad are left in shambles, having to cope with the death of one of their members without the support of their former mentor. Amidst this turmoil, both Quinx Squad and Haise must continue to fulfill their duties to the CCG, whether willingly or not. However, the presence of a mysterious group behind the CCG has been made known to Haise, and certain whispers of corruption have not gone unheard by the Quinx Squad as well.

High school student Yuuichi Katagiri cherishes his close circle of friends, composed of four classmates: Yutori Kokorogi, Shiho Sawaragi, Makoto Shibe, and Tenji Mikasa. However, when the funds for the upcoming school trip are stolen, the incident causes Shiho and Makoto—who had been tasked with collecting the money—to distance themselves from the rest of their class. Soon after, Yuuichi and his friends are deceived into meeting up and knocked unconscious by unknown assailants. After waking, the group find themselves confined in a white room with controversial figure Manabu-kun, who reveals that one of the five has gathered them together to clear their personal debt of twenty million yen. To pay off the amount, they must participate in a variety of psychological games that will test the true nature of their friendship and humanity. Distressed and isolated from the outside world, Yuuichi and his friends need to cooperate to complete the games. But as their concealed feelings and problematic pasts begin to surface, their seemingly unbreakable bond may soon shatter into irreparable pieces.