Seventeen-year-old Makoto Konno (Riisa Naka/Emily Hirst) lives with her family in the Shitamachi area of Tokyo, Japan. Makoto lives with her younger sister, Miyuki (Yuki Sekido/Shannon Chan-Kent), and her aunt, Kazuko Yoshihara (Sachie Hara/Saffron Henderson), is an art restorer at the Tokyo National Museum. When Makoto discovers a message written on a blackboard at her high school, she unknowingly falls upon a mysterious, walnut-shaped object. On her way home, Makoto is ejected into a railroad crossing when she loses control of her bicycle and is struck by a train. However she is transported a few minutes back in time to before the accident. Makoto learns from Kazuko that she has the power to "time-leap", to literally leap through time. At first, Makoto uses her power extravagantly to avoid being late, to get perfect grades on tests, and even relive a single karaoke session for several hours. Makoto soon discovers that her actions can adversely affect others.Makoto ends up using up more of her leaps to recklessly prevent undesirable situations from happening, including an awkward confession of love from her best friend Chiaki Mamiya (Takuya Ishida/Andrew Francis). Eventually, she discovers a numbered tattoo on her arm which counts down with each leap. She determines that the tattoo indicates that she can only leap through time a limited number of times. With only a few time leaps left, she attempts to make things right for everyone. After Makoto impulsively uses her final leap to prevent a phone call from Chiaki asking if she knows about time-leaping, she is too late to prevent her friend Kōsuke Tsuda (Mitsutaka Itakura/Alex Zahara) and his new girlfriend, Kaho Fujitani (Mitsuki Tanimura/Natalie Walters), from being struck by the train when he uses her faulty bike. But time freezes and Makoto discovers Chiaki nearby.
Chiaki confesses that he is from the future and leapt through time to see a painting being restored by Kazuko, as it has been destroyed in the future. While walking in the frozen city, Chiaki hints that his original era occurs after a worldwide catastrophe destroys mankind. He reveals that he has used his final leap to prevent Kōsuke's accident and has stopped time only to explain to Makoto what the consequences will be. Having revealed his origins and the source of the item that allowed Makoto to leap through time, and being unable to return to his time period, Chiaki must disappear. Makoto realizes too late that she loves him as well.
True to his words, Chiaki disappears when time begins again and Makoto is upset. As she tries to come to terms with losing him, she discovers that Chiaki's time-leap had inadvertently restored one time-leap to her: Chiaki had leapt back to the time before Makoto used her last leap. Makoto leaps back safely to the moment when she gained her powers, at which point Chiaki still has one remaining time-leap. She reveals everything that he told her in the future concerning who he is, the ability to leap through time, and his reasons for extending his stay in her time frame. Makoto promises to make sure the painting stays safe so Chiaki can see it in his time. As Chiaki leaves, he tells Makoto he will be waiting for her in the future to which Makoto responds that she will run towards him.