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.

Onmyoudou magic was once a powerful technique used by the Japanese during the second World War in order for them to gain the upper hand and establish their nation as a formidable force. But Japan was quickly defeated after the revered onmyouji Yakou Tsuchimikado caused the Great Spiritual Disaster, an event which plagues Tokyo to this very day. As a result of this mishap, the Onmyou Agency was established in order to exorcise further spiritual disasters and combat the demons that would make their way into the world. Now, Onmyoudou has become far more modern, simplified, and refined for use in a wide variety of applications such as medicine and technology. However, not everyone is able to utilize the magic, as is the case with Harutora, a member of the Tsuchimikado's branch family. Despite an old promise to protect Natsume, the heir of the Tsuchimikado's main family and Yakou's supposed reincarnation, as her familiar, Harutora has no talent and chooses to live a normal life instead. But when a prominent member of the Onmyou Agency attempts to recreate the same experiment which led to Japan's downfall, he decides to make good on his word and fight by Natsume's side.

Shuu Tsukiyama is a ghoul: a creature who eats human flesh, and he likes to enjoy his meals to the fullest. One night, while relishing in the premeditated murder of his dinner, Shuu's much anticipated first bite is disturbed by a sudden flash of light. The flash turns out to be from the camera of high schooler Chie Hori, who presents Shuu with the perfect picture capturing his true nature; the extremely clear shot of a bloody corpse and an overly excited Shuu threatens to expose his ghoul identity, thus Shuu needs to sort out this situation quickly. After Shuu discovers that Chie attends the same high school as him and is even in the same class, the reason behind his feelings of obsession changes from self-preservation to morbid curiosity. As he grows closer to the absent-minded and extremely odd photographer, he challenges them both to learn more about each other's conflicting worlds; Shuu promises that Chie will come out of this experience with a photograph superior to the one she already has.