Shintarou Tokumitsu leads an ordinary high school life while living in a studio apartment just for himself. This changes drastically one morning after he finds something strange on his balcony—an angel from Heaven. The innocent and kind girl named Towa was sent to Earth by God to learn more about humans and their way of interacting. It does not take long for her to get attached to Shintarou, who eventually allows her to live with him. However, the small apartment provides little personal space and privacy, and hiding Towa's real identity from the public proves difficult. As he learns to navigate his new life with Towa, Shintarou's encounters with other girls may only complicate the circumstances.

Specials that followed on the Mai-Otome DVD.

Two years after saving the world from a cataclysmic event, the members of the activist organization Avalanche have gone their separate ways. Tifa Lockhart opens a new bar, and her childhood friend Cloud Strife starts up a motorcycle-based courier service. Although most of their former allies have fallen out of touch, Cloud and Tifa live in fragile peace with their two young wards Marlene and Denzel. Their life together begins to crumble as a contagious plague and overwhelming grief pull Cloud away from his newfound family. While distancing himself through his work, Cloud is attacked by three silver-haired figures in black uniforms who bear a passing resemblance to his bitter rival, Sephiroth. As the antagonistic trio stalks Cloud and brings harm to his loved ones, the former mercenary struggles against his own demons while fighting to protect his family and prevent the will of Sephiroth from returning to the planet.

My-Otome Zwei takes place one year after the events of My-Otome. Arika is now a full-fledged Otome (though still under the tutelage of Miss Maria) and Nagi is incarcerated in a prison somewhere in Aries. The various nations are at peace with one another and plan to hold S.O.L.T. (Strategic Otome Limitation Talks) to discuss limiting the numbers of Otome. A mission to destroy a meteor threatening to collide with Earl sets into motion a chain of events which result in a mysterious shadowy figure attacking Garderobe and several Otome as well as a new, more powerful version of Slave appearing across the planet. To make matters worse, Queen Mashiro disappears following an argument with Arika. The series follows Arika's search for Mashiro as well as Garderobe's attempts to uncover the truth behind the shadowy figure.