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.

Kouta Hasegawa is a completely normal high school student who likes his Pompompurin stuffed animal, a Sanrio character modelled after a Golden Retriever, which his grandmother gave him when he was young. However, an incident in which other kids accused him of being girly for liking Sanrio characters made him ashamed of his attachment to Pompompurin. Through a series of unexpected events, Kouta ends up meeting others at school who also like Sanrio characters—Yuu Mizuno, a flashy boy who is popular with girls; Shunsuke Yoshino, a member of the soccer team; Ryou Nishimiya, an underclassman who is a library assistant; and Seiichirou Minamoto, the student council president. Through his new friends, Kouta learns that there is no need to be embarrassed for liking Sanrio characters; and together, they aim to create a play for the cultural festival in order to transform his normal school life into a sparkly one.

The lives of high school freshmen Haruki Mishima and Towa Honda revolve around studying, clubs, and girls. Amid their hectic routines, romance is certainly budding for the two best friends. Since childhood, Haruki has been pining over Miharu Mashiki, and a chance encounter at the convenience store reignites his feelings. As for Towa, the class representative Mami Mihashi has caught his eye; but unfortunately for him, his affections are not reciprocated. While Haruki's more reserved approach to pursuing Miharu contrasts Towa's persistence with Mami, love seems to be elusive for both. As the months fly by, only time will tell if romance is in the cards for the duo.