"Tokyo Ghoul:re" is a sequel to the original "Tokyo Ghoul" series, continuing the story in a world where ghouls, humanoid creatures that must consume human flesh to survive, coexist uneasily with humans. The narrative picks up two years after the events of the first series, focusing on Haise Sasaki, a mild-mannered investigator working for the Commission of Counter Ghoul (CCG). Sasaki leads a specialized team of investigators known as the Quinx Squad, who have undergone experimental procedures to gain ghoul-like abilities while retaining their humanity. Sasaki struggles with fragmented memories of his past, unaware that he is actually Ken Kaneki, the protagonist of the original series, whose memories were suppressed after a traumatic battle.

As the story progresses, Sasaki and the Quinx Squad are tasked with hunting down dangerous ghouls, including members of the terrorist organization Aogiri Tree. The narrative explores the moral complexities of the CCG's operations, as well as the blurred lines between humans and ghouls. Sasaki's suppressed memories gradually resurface, leading to an internal conflict between his current identity and his past as Kaneki. This tension is exacerbated by encounters with former allies, such as Touka Kirishima and Yoshimura, who recognize him as Kaneki.

The plot intensifies as the CCG launches a large-scale operation to eradicate ghouls, targeting the 24th Ward, a ghoul-dominated underground area. The Quinx Squad faces numerous challenges, including betrayal, loss, and the revelation of deeper conspiracies within the CCG. Sasaki's transformation back into Kaneki becomes inevitable as he confronts his past and embraces his dual nature as both human and ghoul. The narrative delves into themes of identity, morality, and the consequences of violence, as characters on both sides of the conflict grapple with their choices and the impact of their actions.

Key characters include Haise Sasaki/Ken Kaneki, whose journey of self-discovery drives the narrative; the members of the Quinx Squad, each with their own struggles and motivations; and recurring figures from the original series, such as Touka Kirishima, who plays a pivotal role in Kaneki's return to his true self. Antagonists like Furuta Nimura, a manipulative and enigmatic figure within the CCG, add layers of intrigue and conflict to the story. The series concludes with a climactic battle that resolves many of the central conflicts while leaving room for reflection on the ongoing struggle between humans and ghouls.