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".

Masaya takes Ichigo to Inohara Park to show her a large cherry tree that is unusually blooming out of season. The next day, Keiichiro discovers that five cherry trees have been infected by the aliens explaining the early blooming. The Mew Mews set out to destroy them simultaneously, or the trees will release a poison dangerous to Tokyo. Mew Ichigo takes the tree in Inohara Park, where Kish waits for her. A fight keeps Ichigo from attacking the tree, and it begins releasing its poison. Ichigo jumps into the tree and successfully destroys it. After Kish leaves, Mew Ichigo finds Masaya standing behind her after he called out "Ichigo".

Ryou and Keiichiro tell the girls to take a vacation, feeling the final battle is approaching and wanting them to be refreshed. Ichigo, however, cannot find Masaya to enjoy the downtime with. Meanwhile, Kish tells Pie and Tart that he is going to use the Blue Knight's powers rather than waiting for Deep Blue to awaken. Pie disagrees, but Tart is convinced. They release all the chimera animas they have in order to distract the Mew Mews and the Blue Knight, while the aliens search for Masaya. Ryou realizes it is a trap and sends the Mew Mews to find Masaya as well. When the girls eventually find him, he is lying unconscious. Mew Ichigo approaches him, but he transforms into the Blue Knight. All of the strange energy in the city gathers around him and he transforms again, into Deep Blue.