The criminal organization Panther Claw begins attacking train stations in Tokyo in order to extort money from the Japanese government. A police task force, led by Inspector Natsuko Aki, is sent to combat the attacks, which are led by genetically altered super-humans. But their battle is interrupted by the appearance of a shape-shifting heroine calling herself Cutie Honey.
To hide Honey and the I-System from Panther Claw, Honey and Aki are enrolled in an all-girls academy. But the headmistress of the school may be more than she seems.
When Honey learns of the attack on Aki's apartment, she races back to Tokyo to intercede, potentially revealing herself to Panther Claw and to Tsuneni.