In the distant future, mankind has left Earth. On one planet named Earl, some of the "old technology" has survived in the form of nanomachines that allow young female virgins to take the role of Otomes - bodyguards and warriors that serve the royalty of various kingdoms. However, not everyone is content to allow the old technology to be so under-utilized, and there are those who seek to use it for their own nefarious ends. This is the environment in which My Otome is set.

The main character is Arika Yumemiya, a 14-year-old girl who grew up in a rural country. She has traveled to the Windbloom Kingdom in search of her mother, who is said to be a legendary Meister Otome. On arrival to Windbloom, Arika sees Meister Shizuru Viola (also known as the Graceful Amethyst) in combat and decides to become an Otome herself. The rest of the series follows her progress as a student at Garderobe academy and through the machinations of those who seek to overthrow the Windbloom Kingdom.

Different from Mai-HiME, Otomes are normal people, and they can use their powers in front of people. I mean, everyone knows Otome. Even there's a school for becoming an Otome.