Makoto Konno finds herself running late for school on 7/13. Her entire day seems to be one bad incident after another: she fails a surprise test; singes her hair from a cooking class accident; ends up being knocked over by two guys horsing around.
After being on clean-up duty in class and assigned to return text manuals, she makes her way into a science lab after hearing some movements in it. To her bewilderment, no one is there. Intrigued by a small object on the floor, she is momentarily startled and falls on her back when someone enters the room. As her left arm lands on the object, a series of strange images fly past in her mind, before she eventually finds herself lying on the ground alone. She hangs out with her best two buddies in class and tells them of the incident. Neither the ridicules from the playful Chiaki nor the concerning words from the kind Kosuke removes her doubts.
After school, Makoto goes to see her Aunt at an art museum. However, the brakes on her bike give out as she races down a hill, and she ends up hitting a guard-rail, flying into the path of an passing train.
However, instead of dying, Makoto finds herself lying several yards on the way to the train crossing, and watches as the same train goes by. Makoto eventually makes it to her Aunt's workplace, and explains the strange incident. Her Aunt calmly explains that Makoto experienced a 'Time Leap', which allowed Makoto to leap back in time several seconds before the accident that would have killed her.
Makoto finds it hard to believe, and spends the rest of the evening pondering this. Leaving the house, she attempts to leap off the edge of a shallow riverbed...and finds herself having gone back a full day (to the date 7/12). Makoto then stays with the timeline, and lives out day 7/13 again...only this time, making it a perfect day. She arrives early to school, aces her surprise test, and has a classmate named Takase take her place at one of the cooking class stations. This causes him to reap the misfortune that she had previously.
Makoto now starts to exploit more personal gains using her new power, such as turning a one-hour karaoke session with Kosuke and Chiaki into ten hours, and leaping back to have her favorite meal. Just when she feels to be at the top of the world, an unexpected awkward event occurs. At a moment when she is alone with Chiaki, the boy asks if they should be a couple. Embarrassed by the question, Makoto chooses to time leap to unsay his words, and starts to avoid Chiaki in school. Her cowardice gives the opportunity for Chiaki's admirer, Yuri from the same class, to get close to the boy.
Makoto tells her Aunt that she regards Chiaki as a freind, but her Aunt cautions her to be careful with her powers. Makoto soon finds that her actions definitely have an effect on others. Takase has been bullied ever since the cooking class misfortune, and at the height of his rage, he tosses a fire extinguisher at Makoto. Chiaki's brave intervention forces Makoto to time leap to rescue him. To her shock and horror, that only changes the victim to be Yuri. Soon Chiaki starts dating with Yuri, leaving Makoto and Kosuke alone at their usual after-school baseball exercises. Makoto finally realizes she cares about Chiaki and regrets missing the previous chance to accept his confession.
Makoto notes a number tattoo on her arm that appears to decrease over time. Looking at a beautiful, mystical painting restored by her aunt, Makoto tells her that she will no more play with other people's feeling by time leaping. She soon gets a chance to redeem her selfish acts by using time leap to other people's benefits - setting up Kosuke with a shy girl named Kaho. After several failed attempts, Makoto leaps all the way back to 7/13, manages to get Kaho to meet with Kosuke, but the incident leaves Kaho with a sprained ankle. Makoto is however satisfied that she finally achieves something good, while noticing the number tattoo has changed to '01', indicating one remaining leap.
Realizing the date, Makoto goes back to the science room, hoping to figure out who entered the room that day. However, her attention is diverted when she gets a message from Kosuke, who borrows Makoto's bike to take Kaho to his Dad's clinic. This fills Makoto with dread, because she recalls how she nearly got killed by the failed brakes of that bike last time.
Makoto rushes to the same train crossing, but doesn't find Kosuke or Kaho there, to her temporary relief. An unexpected call from Chiaki delays her plan to warn Kosuke by phone. When Chiaki suddenly asks her if she has been time leaping, the shocked Makoto uses her last leap to undo his question. As she finishes the call, Kosuke and Kaho ride by, and Makoto chases after them in a mad panic, watching as Kosuke struggles to brake, before both he and Kaho hit the guard rail, flying into the path of the oncoming train.
Makoto shuts her eyes in desperation, pleading for time to stop. Opening her eyes, she sees the world is frozen in time, and Chiaki is there to meet her, with her bike in hand. Chiaki then explains that he can time leap as well, and that he took Makoto's bike to save Kosuke and Kaho. Chiaki then explains that he is from the future, and that he originally travelled back in time to see a destroyed painting, but has been kept waiting as it was being restored. Meanwhile he has met Kosuke and Makoto and find their company hard to desert. Chiaki mentions that the strange object that Makoto saw on the floor in the science lab was a charger. This gave Makoto the ability to time leap. Each charged person has a specific number of time leaps (the tattoo on Makoto's arm is a counter regarding how many leaps are left). Makoto has used all hers up, and upon saving Kaho and Kosuke, Chiaki has as well. Because of this, he has no way to return to the future, and because he has revealed these secrets, he tells Makoto he has to disappear. When time unfreezes again, Makoto finds Chiaki has vanished.
The next day at school, Chiaki doesn't show up for class, and many speculate what has happened to him. Kosuke talks this over with Makoto, who is now in deep sorrow that she seems to have made a mess of everyone's life, and that Chiaki is gone forever.
That night, Makoto looks at the tattoo on her arm, and is amazed to see that it has been restored to '01'. Chiaki's time leap cancelled out her last leap the previous day! Enlightened and enpowered, Makoto makes a big leap back to 7/13 to correct her wrongs once and for all. Makoto tells Yuri how she really likes Chiaki. She tells Kosuke to invite Kaho and her friends to join their baseball practices, and also warns him not to use her bike. Finally, Makoto meets with Chiaki, and confirms that he still has one leap left, as well as explaining what she knows from him. She promises to preserve the painting for Chiaki to see in the future.
Now his cover blown, Chiaki has to return to the future. Makoto never gets to hear his confession again, and is heartbroken to see him go. Chiaki whispers to her that he will be waiting for her in the future, to her great joy.
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