The number of terrorist acts in Japan has never been lower, thanks to the efforts of a syndicate called Direct Attack (DA). The organization raises orphaned girls as killers to carry out assassinations under their "Lycoris" program. Takina Inoue is an exceptional Lycoris with a strong sense of purpose and a penchant for perfection. Unfortunately, a hostage situation tests her patience, and the resulting act of insubordination leads to her transfer out of DA. Not thrilled about losing the only place she belonged to, she reluctantly arrives at her new base of operations—LycoReco, a cafe in disguise. Takina's new partner, however, turns out to be quite different from what she imagined. Despite being the famed Lycoris prodigy, Chisato Nishikigi appears almost unconcerned with her duties. She drags Takina along on all kinds of odd jobs under the simple explanation of helping people in need. Takina is even more puzzled when Chisato takes down a group of armed assailants without killing any of them. Feeling like a fish out of water, Takina itches to get reinstated into DA—but Chisato is determined to prove to her that there is more to a life than just taking them.

Ichigo Momomiya is excited to start high school and fall in love. She is in luck when she meets the popular and good-looking Masaya Aoyama, and she immediately develops a crush on him. When Ichigo learns that Aoyama is passionate about the environment, she seizes the chance to ask him out thanks to some tickets to an exhibition about endangered animals. During their date, Ichigo is struck by a mysterious light and faints. Waking up to the sight of Aoyama, she remains unharmed—but they both must escape from a giant rat-like creature after it injures Aoyama. To save her crush, Ichigo awakens her powers and transforms into a heroine with the skills of a cat. After she defeats the monster, researchers Ryou Shirogane and Keiichiro Akasaka explain that Ichigo was chosen to become a part of the Mew Project: a group of five magical girls whose DNA has been infused with those of certain endangered species. Now, Ichigo must find the rest of her teammates to defeat the Chimera Anima—beings infected by aliens who want to take over the world—before it is too late.

After fending off the threat of a Neuroi invasion of Romagna and destroying the enemy's nest over Venezia, Yoshika Miyafuji goes back to her home town in the Empire of Fusou. Despite the loss of her magical and healing abilities, the former officer of the 501st Joint Fighter Wing wants to continue studying medicine. This is in order to help those in need, both civilians and those on the front lines alike. She receives an invitation from a prestigious school in Europe and decides to accept the offer, embarking on a journey back to the war-torn continent. However, a new danger arises, as more and more Neuroi manage to break through human defense lines, appearing unnoticed in supposedly safe areas and disturbing the balance of power in Europe. Yoshiki's sense of duty collides with her inability to pilot a Striker Unit, but with her friends in peril, it seems that there is only one thing she can do.

On a whim, first-year Ayumu Tanaka quits the Kendo Club to join the illegitimate Shogi Club. Urushi Yaotome, the president of the club and a master of shogi, is thrilled to finally have a playing partner. As Ayumu's upperclassman, Urushi endeavors to be his shogi mentor and student role model. Too often, however, she finds herself blushing with embarrassment! Stone-faced and honest, Ayumu sees no issue with calling Urushi "cute." Although Ayumu likes her, he refrains from confessing and promises himself to first beat her in a game of shogi. Through school life and shogi games, the two students have many hilarious and heart-warming adventures. Ayumu enjoys every second with Urushi, but he is still a long way from beating her in shogi. With the commitment he made to himself, will Ayumu ever get the chance to confess his feelings to Urushi?