Ryou and Keiichiro tell Ichigo that the creature she saw was a parasitic alien, called a chimera anima. To stop them, the Mew Project infused five girls with the DNA from specific endangered species, enabling the girls to become "mew mews". Ichigo begins working at Cafe Mew Mew while searching for the other four girls who bear the Mew marks. Keiichiro gives her a robot, Masha, to help with her work. While going home, Ichigo meets Mint Aizawa and her dog. Later, Ichigo visits Mint's home to return a handkerchief, but Mint's dog becomes infected by a chimera anima. During the battle, Ichigo discovers that Mint is the second mew mew, Mew Mint. They defeat the monster, returning the dog to normal. Mint joins Ichigo in working at the café.

Mint is upset by Zakuro's rejection, and the others try to cheer her up. Ichigo and the others go to talk to Zakuro. Meanwhile, Kish approaches Zakuro and offers her a deal to return her body to normal if she joins him. When the girls arrive, Kish traps Mint, Lettuce, and Pudding in an alternate dimension. He then demands a fight between Ichigo and Zakuro in exchange for the trapped friends. Ichigo refuses and returns to the café where Ryou encourages her to trust in Zakuro and share her feelings. While shooting a television show, Zakuro is attacked by a chimera anima. Ichigo arrives and battles the monster while Zakuro saves the others. After its defeat, Zakuro agrees to be a part of the team. Apparently, the entire battle was aired on live television, and so they introduce themselves to Tokyo as the protectors of justice, "Tokyo Mew Mew".

The group is searching for mew aqua around a large rock formation in the forest when the girls and Masaya get separated. Something strange begins happening and everyone transforms. Masaya transforms into the Blue Knight, but falls from the rock and returns to normal. Kish confronts him and reveals that he cannot maintain his Blue Knight form if he is not protecting Ichigo. The alien moves to kill Masaya, but Mew Ichigo transports and appears between them. Masaya is knocked unconscious as Kish tries to kill Ichigo. This triggers Masaya's transformation, but his powers go out of control due to his rage at Kish. The other Mew Mews teleport to Mew Ichigo just in time to put up a shield around her as the rock explodes from the Blue Knight's power. Masaya returns to normal, seemingly unharmed. Kish tells Pie and Tart that the Blue Knight is the one who can save them.