In an alternate universe, everyone has a secondary gender: alpha, beta, or omega. From these, there is a natural hierarchy. Alphas are at the top, while omegas are at the bottom due to their lack of control over releasing pheromones that can dangerously attract other genders, especially alphas.

Megumi Kokonoe is an elite alpha. However, his behavior is reflective of little other than juvenile delinquency. When his subordinates are attacked by a masked man, Megumi does what any good leader would do—he sets out for revenge. Despite the mysterious man's ability to take down the alpha students of Kokonoe Academy, Tsugumi Yamada, an omega, shows up to the confrontation absolutely reeking of pheromones. It turns out that unlike other omegas, Tsugumi rejects the use of suppressants and controls his heat with only his willpower.

Believing all alphas view omegas as nothing more than tools for reproduction, he holds an intense hatred for them. When Megumi makes it extremely clear he does not feel that way—and confesses feelings that Tsugumi does not understand—Tsugumi starts to doubt the strength of his willpower alone.