The story follows Ken Kaneki, a student who barely survives a deadly encounter with Rize Kamishiro, his date who reveals herself as a ghoul. He is taken to the hospital in critical condition. After recovering, Kaneki discovers that he underwent a surgery that transformed him into a half-ghoul. This was accomplished because some of Rize's organs were transferred into his body, and now, like normal ghouls, he must consume human flesh to survive. The ghouls who manage the coffee shop "Anteiku" (あんていく) take him in and teach him to deal with his new life as a half-ghoul. Some of his daily struggles include fitting into the ghoul society, as well as keeping his identity hidden from his human companions, especially from his best friend, Hideyoshi Nagachika.
The prequel series Tokyo Ghoul [Jack] follows the youths of Kishou 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 at 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 result of horrific brain damage sustained from Kishō Arima). He is the mentor 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.