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.

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.

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.

Chizuru, a cheerful girl with a history of unsuccessful romance, is planning to break up with her boyfriend, Yuudai, since he never seems to reciprocate her feelings. However, as she arrives at what she plans to be their final date, Yuudai presents her with a gift that turns out to be an energetic and troublesome mini donkey. While Yuudai was hoping that today would be the day he could finally summon enough confidence to let Chizuru know the depth of his feelings, a series of misunderstandings threaten to tear the couple apart forever. With a rambunctious mini donkey doing its best to mend their relationship, Chizuru and Yuudai each wonder if they are capable of loving and being loved in return.