My-Otome Zwei takes place a year after the events in My-Otome. Arika has become a fully trained Otome, guided by Miss Maria, while Nagi is serving time in an Aries prison. Peace reigns among the different nations, and the Strategic Otome Limitation Talks are on the horizon, with the goal of reducing the number of Otomes. However, a natural disaster is about to occur when a meteor threatens to hit Earl. A mission is launched to destroy it, but this causes a mysterious figure to attack Garderobe and other Otomes. A new and more potent version of Slave also emerges, causing even more chaos. Queen Mashiro goes missing after an argument with Arika, making matters worse. The series focuses on Arika's search for Mashiro, while Garderobe investigates the shadowy figure and their true intentions.