The story follows Eren Yeager and Mikasa Ackerman entering Titan Jr. High, a school where humans and Titans study in the same area in coexistence. Because of a "traumatic" event, where the Colossal Titan ate his lunch back in middle school, Eren hates the Titans, and is constantly trying to find a way to rid the earth of their kind. Because of this, he has a hard time making friends, much to Mikasa's worry.

Tokyo has been decimated by a terrorist attack, the only clue to the culprit's identity is a bizarre internet video. Two mysterious children form Sphinx, a clandestine entity determined to pull the trigger on this world.

When Tsukune accidentally enrolls in a school for monsters disguised as humans, he must hide the fact that he's really human or risk losing his life.