Seventeen-year-old Makoto Konno (Riisa Naka/Emily Hirst) lives with her family in the Shitamachi area of Tokyo, Japan. Makoto lives with her parents and younger sibling Miyuki (Yuki Sekido/Shannon Chan-Kent). Her aunt Kazuko Yoshiyama (Sachie Hara/Saffron Henderson), is an art restorer at the Tokyo National Museum. One day, when Makoto discovers a message written on a blackboard at her high school, she inadvertently falls upon a mysterious, walnut-shaped object. On her way home, Makoto is ejected into a railroad crossing when the brakes on her bicycle fail and is struck by a train. She is transported a few minutes back in time to before the accident. Kazuko explains to Makoto 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 an entire hour, but Makoto soon discovers that her actions can adversely affect others.
Makoto ends up using up most of her leaps frivolously, to prevent undesirable situations from happening, including an awkward love confession from her best friend Chiaki Mamiya (Takuya Ishida/Andrew Francis). Makoto eventually discovers a numbered tattoo on her arm which counts down. She determines that the tattoo indicates that she can only time leap a limited number of times. Using her remaining time leaps, Makoto attempts to make things right for everyone. Makoto impulsively uses her final leap to prevent a phone call from Chiaki asking if she knows about time-leaping. Due to this, she arrives 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 a train when they borrow her faulty bike. However, time suddenly freezes and Makoto discovers Chiaki nearby.
Chiaki confesses that he is from the future, the walnut-shaped object is a time-traveling device and he used it to leap through time to see a painting that is being restored by Kazuko, as it has been destroyed in the future. While walking with Makoto in the frozen city, Chiaki explains that he stayed longer in her time frame than he originally planned. He admits to using 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, the nature 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.
True to his words, Chiaki disappears when time begins again. Initially distraught at losing Chiaki, Makoto discovers that Chiaki's time-leap had inadvertently restored a time-leap to her: Chiaki had leapt back to the time before Makoto used her final leap. Makoto leaps back to the moment when she gained her powers, at which point Chiaki still has one remaining time-leap. Makoto explains to Chiaki that she is from the future and reveals everything he told her 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. Before Chiaki leaves, he tells Makoto that he will be waiting for her in the future. When Kōsuke asks her where Chiaki went, she says that he went to study abroad, and that she made a decision about her own future.