The overarching plot reveals that the human-ghoul conflict was orchestrated from the shadows. Rize's steel beam "accident" in Episode 1 was intentionally engineered by Furuta Nimura and the Clowns to allow Dr. Kanou to create half-ghoul hybrids. The CCG's ruling family, the Washuu Clan, are secretly ghouls themselves who controlled Tokyo's law enforcement to keep both species in a controlled loop of slaughter.
Kishou Arima and Eto Yoshimura (the One-Eyed Owl) were secret co-conspirators who created the legend of the "One-Eyed King" as a symbol to eventually unite ghouls. Furuta later forces Kaneki to consume massive amounts of Oggai squad ghouls, mutating Kaneki into a colossal biological parasite named "Dragon" that destroys Tokyo. Dragon's toxins turn normal humans into ghouls, rendering the biological boundary obsolete.
In the finale, Kaneki destroys Dragon and defeats Furuta. Humans and Ghouls unite to save their shared city, discovering synthetic food substitutes that allow ghouls to eat without harming humans, creating an era of true coexistence.