Ryuko Matoi is a vagrant school girl traveling from place to place searching for clues to the truth behind her father's death - the "woman with the scissor blade". The journey leads Ryuko to Honnouji Academy.

Weakened by her battle, Ryuko flees Honnouji Academy before collapsing in the street. Rescued, she's given food and shelter for night, and upon returning to the Academy faces off against Omiko Hakodate, the Girls' Tennis Club Captain, to repay the favor.

Having kept her end of the bargain, Ryuko demands answers from her homeroom teacher, Aikuro Mikisugi, and learns the secret behind the power of Senketsu and the Goku Uniforms. Meanwhile, Satsuki Kiryuin returns home to claim a power of her own.

Sirens awaken the No-Star students for the start of “No-Late Day,” where being tardy will get you expelled from Honnouji Academy. With Senketsu in the wash, Ryuko must fight on her own to get through the Discipline Committee’s traps and arrive on time.

A mysterious man arrives at Honnouji Academy and quickly proves himself to be more than capable of fighting against a Two-Star Goku Uniform. But when he sets his sights on Ryuko, who will be left standing?

Overwhelmed by recent events, Ryuko demands answers from her homeroom teacher, Aikuro Mikisugi. Meanwhile, Uzu Sanageyama, Honnouji Academy’s Athletic Committee Chair and on the Elite Four, makes a request of his own… to challenge Ryuko to a duel!

Mako is offered a better life away from poverty. To do so she must don a suit and face Ryuko in combat.

It's graduation at Honnouji Academy, but not everything is as it seems. Ryuko Matoi and the gang must defeat their final enemy.