My-Otome Zwei is set one year after the events of My-Otome, during which time Arika has become a full-fledged Otome but remains under Miss Maria's guidance as she hasn't earned enough credits to graduate yet. Nagi is currently imprisoned in Aries. The nations are at peace with each other and plan to hold S.O.L.T. (Strategic Otome Limitation Talks) to discuss limiting the number of Otomes.
A mission to destroy a meteor that threatens to collide with Earl sets off a series of events, including the appearance of a mysterious shadowy figure who attacks Garderobe and several Otomes. Additionally, a new, more powerful version of Slave emerges 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 efforts to uncover the truth behind the shadowy figure.