Peace has returned to Honnouji Academy at last, and now that it has served its original purpose, the unique high school is set to be shut down within a month. However, there is still one final event that must take place: the graduation ceremony. As each member of the student council prepares to leave their past selves behind to focus on what they would like to do in the future, Satsuki Kiryuuin struggles to find her own path, having lost her resolve after finally achieving victory.

But just before she is to give her speech to the student body, the ceremony is disrupted by mysterious beings that are identical to the student council members. As Ryuuko Matoi and the Elite Four prepare for battle once more, they quickly discover that the one pulling the strings is an old enemy who has returned to take revenge.