I'm, Asahina Mirai! Everyone, do you know about the "Wishing Stone"? It's a powerful stone that can grant any wish you want! Today is the day we're celebrating its revival, a huge magic festival that only occurs once a century♪ Together with Liko and Ha-chan, I wish upon this "Wishing Stone", but believe or not, it chose Mofurun's wish! This is truly exciting!! However...a mysterious bear・Dark Matter suddenly appears, and takes Mofurun with him!! I have to definitely save Mofurun! Even when we're separated, the wishes of all of us can bring about miracles!! Well that is what I thought, what~~~!! Mofurun became a Pretty Cure~!?

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.

In the distant future on the planet Earl, colonized by immigrants from Earth centuries ago. "Old technology" has survived in the form of nanomachines that allow female virgins wield Highly-advanced Materializing Equipment (HiME) and become Meister Otomes - bodyguards and warriors that serve the royalty of various kingdoms.

Arika Yumemiya has come to Windbloom Kingdom in search of her mother, whom Arika knows was an Otome. On her arrival she meets the top Coral Otome student, Nina Wáng, and Windbloom's heir to the throne, Mashiro Blan de Windbloom. The series follows Arika's progress as a student at Garderobe Academy and the machinations of those desiring the destructive power of the old technology for themselves.

Yumemiya Arika has travelled far in search of her goal — the prestigious Garderobe Academy. This is the school where young girls are trained to become Otome, protectors of royal leaders throughout the lands.