The story takes place in Tokyo Butei High School, a special school where armed detectives—"Butei"—are trained to use weapons. Kinji Tooyama is a second-year-student who has a special ability, but he keeps it a secret to maintain an ordinary, peaceful life; however, when he gets caught in a bombing on the way to school, he encounters H. Aria Kanzaki, the most powerful S-Rank Butei student in Assault Studies.

More than twenty years ago, an evil summoner committed "Great Summon". One third of human beings were killed, and devils and monsters invaded the Earth. One day, a painter, Tamura Fukutaro, moves into an apartment house called "Ashiaraiyashiki" and gets involved in the troubles of his non-human neighbors. It's the beginning of a severe battle among gods, devils and the ruler "The Central".

In Thrace, Arion is taken from his mother Demeter by the god Hades. In the Underworld, Arion is trained to be a warrior. His training is driven by revenge: Arion was told that his mother's blindness was caused by Zeus and Zeus' death will remove the curse. Finally, Arion and Geedo (a huge ape-like creature who had become Arion's friend and companion) left the Underworld to find Zeus. Seneca, a small thief, makes off with Arion's sword and this leads Arion to his first encounter with the forces of Zeus, commanded by his daughter Athena. Arion is captured but is later set free by Lesfeena, Athena's mute serving girl. As Arion rejoins Geedo and Seneca (and worries about Lesfeena), the forces of Zeus and Poseidon face each other in battle. In the background sits the scheming Hades, and the calm Apollon who seems to have plans of his own.

Koro-sensei reminisces about his first meeting with Karasuma, where they first butted heads and fought against each other, ultimately coming to respect one another. However, Karasuma eventually points out their actual meeting wasn't nearly as eventful.