In 2008, the Japanese government began hunting people who identify as otaku in an effort to protect the country's culture. In just one week, the enforcement agency known as the SSC captured almost every otaku by force and confiscated their memorabilia. One passionate man calling himself Otaku Hero refuses to allow this agency to do as they please: he raises a resistance army made up of other displaced geeks who band together to help defend their culture.

Three years later, the fires of rebellion wane as all hope seems lost for otakus. Spurred on by his ally—the magical girl Anarchy—Otaku Hero commands the resistance in an effort to reunite Anarchy with the other two other magical girls: Blue and Pink. By combining the power of this trio, the resistance may be able to defeat the SSC and save otaku culture for everyone.