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.

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!

Satsuki Kiryuin joins the front line of Osaka to battle Kaneo Takarada, the heir to the Takarada Conglomerate. Using the influence of money, Takarada rallies the locals to fight, but Satsuki is suspicious there is another power behind the city's defense.

The Honnouji Academy Cultural & Sports Grand Festival comes to an abrupt and very unexpected conclusion! Battle lines are drawn and Ryuko must decide who is friend and who is foe. But will she have the power to resist the power of the Life Fiber?

A surprising turn of events catches Nui Harime off guard and gives Nudist Beach a chance to regroup and plan their next step in the fight against Ragyo. But will Ryuko and Satsuki be able to settle their recent conflicts?

The ongoing battle presses towards Honnouji Academy, but Ragyo and the Original Life Fiber stand in the way. Ryuko and Satsuki set off to face them, leaving Nudist Beach's defense to... Mako?! Meanwhile, a crazed Nui continues working feverishly...

The final confrontation is at hand! Will Ragyo and Nui bring on the end of the world, or will Ryuko and the others be able to stop them?