My-Otome Zwei is set one year after the events that occurred in My-Otome. Arika is now a fully-fledged Otome but still receiving guidance from Miss Maria as she has yet to earn adequate credits to graduate. Nagi is imprisoned in a distant prison in Aries, and the various nations are at peace with each other. They plan to hold talks to limit the number of Otome under Strategic Otome Limitation Talks (S.O.L.T.). However, when a mission to destroy a potentially dangerous meteor is launched, an unknown being attacks Garderobe and several Otome. Also, a newer, more robust version of Slave emerges across the globe. Queen Mashiro goes missing after an argument with Arika, and the story follows the efforts of Arika and Garderobe to find her and unravel the mystery behind the shadowy attacker.