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.

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.