With a single, hopeful wish, young women can become magical girls and take on the thankless task of getting rid of the hidden chaos of the world. Despite this, the magical girls of Mitakihara are enjoying themselves, leading normal middle school lives by day and working together as a brilliant magical girl team by night.

And yet... was the world always this way? Were the battles of magical girls supposed to be like this? These are the thoughts of Homura Akemi, a very shy girl who has recently transferred schools and became a member of the Mitakihara magical girls. The seemingly perfect lives that she and her friends lead has caused Homura to start doubting and observing the world. And as she slowly isolates herself from the group to explore the world in secret, she finds that things are not what they seem—after all, one of these girls shouldn't even exist...