The story follows Ken Kaneki, a college student who barely survives a deadly encounter with Rize Kamishiro, his date who reveals herself as a ghoul, a human-like creature that hunts and devours human flesh, and is taken to the hospital in critical condition. After recovering, Kaneki discovers that somehow he underwent a surgery that transformed him into a half-ghoul by transferring some of Rize's organs into his body, as she died when she attacked him, and just like them, he must consume human flesh to survive as well. With no one else to turn to, he is taken in by the ghouls who manage the coffee shop "Anteiku", who teach him to deal with his new life as a half-human/half-ghoul, including interacting with ghoul society and its conflicting factions, while striving to keep his identity secret from other humans.
The prequel series Tokyo Ghoul: JACK follows the youths of Kishō Arima and Taishi Fura, two characters from the main series who become acquainted when they join forces to investigate the death of Taishi's friend by the hands of a ghoul, leading to Taishi eventually following Arima's path and joining the CCG (Commission of Counter Ghoul), the federal agency tasked into dealing with crimes related to ghouls as well.
The sequel series Tokyo Ghoul:re follows an amnesiac Kaneki under the new identity of Haise Sasaki, the leader of a special team of CCG investigators called "Quinx Squad", that underwent a similar procedure as his, allowing them to obtain the special abilities of Ghouls in order to fight them, but still being able to live as normal humans.