After a successful showdown at Tokyo Tower, the Mew Mew girls enjoy a temporary respite. Now that Ichigo Momomiya and Masaya Aoyama have confessed their feelings to each other, Ichigo is overjoyed to spend time with her new boyfriend. However, their quick break gets interrupted, and soon the girls must battle against the Chimera Anima yet again. When things go awry in the ensuing fight, Ichigo is placed in grave danger. Just when things look most bleak, the mysterious Blue Knight arrives and saves Ichigo, proclaiming that he was born to protect her, before disappearing into thin air. With the fate of the world on their shoulders and the identity of the Blue Knight in question, the Mew Mew girls must strive to create balance between alien-fighting and their personal lives.

Two years have passed since the CCG's raid on Anteiku. Although the atmosphere in Tokyo has changed drastically due to the increased influence of the CCG, ghouls continue to pose a problem as they have begun taking caution, especially the terrorist organization Aogiri Tree, who acknowledge the CCG's growing threat to their existence. The creation of a special team, known as the Quinx Squad, may provide the CCG with the push they need to exterminate Tokyo's unwanted residents. As humans who have undergone surgery in order to make use of the special abilities of ghouls, they participate in operations to eradicate the dangerous creatures. The leader of this group, Haise Sasaki, is a half-ghoul, half-human who has been trained by famed special class investigator, Kishou Arima. However, there's more to this young man than meets the eye, as unknown memories claw at his mind, slowly reminding him of the person he used to be.

A sinister threat is invading Tokyo: flesh-eating ghouls who appear identical to humans and blend into their population. Reserved college student Ken Kaneki buries his nose in books and avoids the news of the growing crisis. However, the appearance of an attractive woman named Rize Kamishiro shatters his solitude when she forwardly asks him on a date. While walking Rize home, Kaneki discovers she isn't as kind as she first appeared, and she has led him on with sinister intent. After a tragic struggle, he later awakens in a hospital to learn his life was saved by transplanting the now deceased Rize's organs into his own body. Kaneki's body begins to change in horrifying ways, and he transforms into a human-ghoul hybrid. As he embarks on his new dreadful journey, Kaneki clings to his humanity in the evolving bloody conflict between society's new monsters and the government agents who hunt them.

Ichigo Momomiya expected her date with her crush, Masaya Aoyama, to have a more romantic ending than her falling asleep after she sees a vision of a cat entering her body. Things get even stranger when, the next day, she begins displaying cat-like behaviors such as an intense craving for fish. When Masaya is attacked by a monster, she discovers that she is able to transform into the cat-eared magical girl, Mew Ichigo. After she saves Masaya, two researchers named Ryou Shirogane and Keiichiro Akasaka approach her and reveal they had injected her with Iriomote Cat DNA in order to create a magical girl that can save the world from aliens. Ichigo is tasked with fighting these monsters, but saving the world proves to be just too much for Ichigo to handle by herself. Fortunately, she learns that there are four other girls just like her, and now, Ichigo must find them quickly before the aliens completely take over the planet.