Thirteen-year-old Ichigo Momomiya is at an exhibit showcasing endangered animals with her crush Masaya Aoyama when a strange occurrence takes place. A beam of light hits her and she sees a cat enter her body. The next day, she starts to show cat-like behavior. During a subsequent attack on Masaya by a mammoth creature, Ichigo transforms into a magical girl with a pink ensemble, a tail, and cat ears.
Ryou Shirogane informs Ichigo that what she encountered was a dangerous alien known as a Chimera Anima. These beings infect animals, turning them into massive monsters. Ryou and Keiichiro Akasaka, the owner of Cafe Mew Mew, concocted the Mew Project, an initiative in which they would use DNA from five Red Data animals to produce biological weapons that could combat the Chimera Anima. However, due to an earthquake that struck the museum the previous day, the experiment went awry, and the DNA ended up inside Ichigo and four other girls.
As a result, Ichigo is now considered a biological weapon and must work alongside her new comrades to defeat the aliens. She must also conceal her feline identity from Masaya.