The story opens up showing Mikuru's daily life working as a mascot character in a local shopping district while the narrator explains Mikuru's mission on Earth to protect Itsuki from danger. After receiving her pay, Mikuru travels the streets before secretly keeping an eye on Itsuki Koizumi, a seemingly normal high school boy. Itsuki is an esper, but his powers have not awakened yet. Mikuru is relieved Itsuki's safe and goes on to more work at the butcher shop and later returns to the stationary shop she's been living at for some well-deserved sleep.
Yuki Nagato, an evil magician/alien, makes her appearance before the scene abruptly switches to a confrontation between Yuki and Mikuru, who is now in a waitress uniform. Mikuru claims she'll protect Itsuki no matter what before firing (toy) guns at Yuki. Yuki blocks the shots with her magic wand called the Stirling Inferno. Mikuru drops her weapons and decides to use her trump card, "Mikuru Beam", which is an attack that comes from Mikuru's left eye. The screen goes black before Yuki suddenly pushes Mikuru down on the ground and covers up Mikuru's eye with her hand and a voice complains offscreen wondering what on Earth Yuki thinks she's doing.
The scene switches to an ad placement for "Ohmori Electronics" done by Mikuru in her bunny suit and Yuki standing behind her with a sign with the store's name on it.
The scene switches again to Mikuru in her waitress outfit walking down a street as the narrator explains Yuki defeated her in that confrontation. She goes back to the stationary store to change into her bunny suit and go back to work. Itsuki, meanwhile, is walking down a vacant street before Yuki suddenly appears. Yuki explains what she is and that Itsuki has a hidden power that she wants. Yuki uses the Stirling Inferno on Itsuki but Mikuru suddenly pushes Itsuki out of the way of the attack before she accidentally runs into a light pole. Holding her eye in pain, Mikuru says she won't let Yuki have her way. Yuki leaves leaving Itsuki and Mikuru still in the street. Itsuki asks who Mikuru is and she claims she's just a bunny girl who happened to come along. Mikuru runs off leaving Itsuki to wonder who she really is.
The scene shifts abruptly again to another confrontation between Mikuru and Yuki near a lake. Yuki sends three people under her control after Mikuru resulting in Mikuru and one of the mind-controlled boys into the water. Mikuru was unable to do anything to stop them after all. Itsuki appears in the scene and helps Mikuru out of the water. Mikuru faints while explaining to Itsuki why she was there and Itsuki picks her up in his arms and carries her off to his home.
After laying Mikuru down to sleep, Itsuki is about to kiss the unconscious Mikuru when Yuki suddenly appears at the window. Yuki presents Itsuki with two choices but Itsuki claims he needs more time to decide. Yuki leaves and the narrator explains that Itsuki and Yuki seem to have an understanding now.
The scene switches to another ad placement, this time for "Yamatsuchi Model Shop".
More scenes seem to have been skipped for now Mikuru is living with Itsuki at his house and Yuki has begun attending Itsuki's high school. Yuki tries various approaches to get Itsuki to fall for her but none seem to work. Mikuru eventually transfers to Itsuki's high school as well, resulting in yet more confrontations between Yuki and Mikuru.
Yuki and Mikuru have a final confrontation on the school's roof. Yuki's final attack hits Mikuru who collapses. Itsuki rushes over to her and pleads with Yuki to stop this fight. Yuki uses the Stirling Inferno on Itsuki but his powers suddenly awaken and send Yuki flying off. Itsuki and Mikuru have returned peace to the world with a happy ending as their reward.
As the credits roll, a boy looks at the screen in shock and disgust while Mikuru sits next to him. Itsuki and Yuki are watching the screen as well. A girl suddenly jumps up in front of the screen seeming to be extremely pleased with the completed movie. She says that it was extremely well done and asks Kyon, the narrator, if he thinks so too. Kyon looks disgusted and horrified at the idea of showing this movie to the public.