In the opening, a comet fragment is seen falling through the layers of clouds in the sky. It appears to fall on the town below it but that is left ambiguous as it cuts to the two main characters, Taki and Mitsuha, talking about how they feel as if they are missing something and that the feeling had lingered since the day that "The stars came falling... It was nothing more, nothing less than a beautiful view."

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Mitsuha Miyamizu, a high school girl living in the fictional town of Itomori in Gifu Prefecture's mountainous Hida region, is told by multiple of the people around her that she acted strangely the previous day, while noting that she is normal today. That night, she performs a ritual for her grandmother which is scorned by her classmates. Frustrated at her boring and close-knit life, she screams out on the shrine steps that "I hate this place! I hate this life! Please make me a handsome Tokyo boy in my next life!" much to her sister, Yotsuha's dismay.

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The next day, she wakes up in an unfamiliar place, realizing that she is in the body of a boy called Taki Tachibana. Leaving the house, she realizes that she has ended up in Tokyo, as if her dream had actually come true. She enjoys her time in his body, but only half-heartedly attempts to retain Taki's reputation, as she believes it is all just a 'very realistic dream.'

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Taki returns to his own body, upon which he is continuously shocked by the changes Mitsuha has made, from leaving a 'thanks to my feminine powers' memo in his electronic diary to fixing his crush and coworker, Miki Okudera's, skirt with threads. At the same time, Mitsuha finds that back in Itomori, Taki got angry at several of her classmates after mocking Mitsuha (which he took to be an insult to himself) and channeled his anger by kicking down a desk in the classroom. Both, shocked, flip through their books and notes, and come to the same conclusion: That in their dreams, they are switching bodies.

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Through a series of rushed cut scenes, it is shown that Taki and Mitsuha start communicating with each other by leaving notes on paper or leaving memos in each other's phones. Both continually voice their frustrations with one another, first, with Mitsuha telling Taki to 'watch the skirt', after which Taki tells Mitsuha to stop wasting his money at cafes, which she rebuts that it's his body that's eating and that she's working too. Mitsuha helps Taki develop a relationship with Miki, which he tells her to stop changing his relationships, soon after which Mitsuha frantically asks him why a girl is in love with her. He replies that she is more popular when he is in her body, where she tells him "Don't be so full of yourself - not like you have a girlfriend!" after which Taki points out she doesn't have a boyfriend. The sequence ends with them both comically writing on their faces, and saying, "I'm single because I want to be!"

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Taki wakes up in Mitsuha's body again one day. He is made to walk up a tall mountain that oversees the entire town of Itomori to bring the girls' 'kuchikamizake' to the shrine, by Mitsuha's grandmother, Hitoha, and even ends up having to carry her. During the journey, Mitsuha's grandmother tells him and Yotsuha about 'Musubi', that it is the very fabric of time and life itself. At the shrine(which is inside a large rock encircled by two oddly symmetrical streams of water at the top of the mountain), He is told it is 'half of Mitsuha', to which he shudders. He looks at the view of the town from one of the points on the mountain and decides to tell Mitsuha to go there to watch the view.

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One day, Taki wakes up back in his body, and finds that Mitsuha has actually set up a date for him and Miki, which he is utterly unprepared for. The date goes very shakily, during which they go to a 'Nostalgia' exhibition and Taki is attracted by several pictures of Itomori under the Hida section. At the end, Miki notes that even though they both used to like each other, Taki now likes someone else, which he embarrassedly says is not true (although seemingly increasing her belief of that). He looks in the sky, trying to see the comet Mitsuha had said would be overhead. Not being able to see it, he frustratedly tries to call Mitsuha.

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The movie then cuts to Mitsuha on the morning of her town's festival, which is the day the comet will be, according to multiple newscasts before this, most easily visible from Earth. Her friends experience shock seeing that she has cut her hair, but she shrugs it off and brings them to the place Taki recommended to see the comet. She shouts excitedly that she can see the comet, but suddenly, the comet splits. She stands there shocked. It then cuts to Taki, who then notes after that, the body-switching stopped, after disappointedly hearing the 'This person's phone number does not exist or has their phone turned off' message trying to call Mitsuha.

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Taki decides to go find Itomori so he can meet Mitsuha. Not knowing it's name nor location, he relies solely on the drawings he made of the town. He, followed by his friend Tsukasa and Miki, travels through the Hida region trying to find it. Having given up, he decides to return to Tokyo, but a Ramen restaurant's owner, whose store he stops at, notices his drawing and tells him it is Itomori; but when Taki says that it is the town he's looking for, the whole group notes to him - that Itomori was destroyed by a fragment of the comet Tiamat when it passed three years ago. Unbelieving, he goes to the now derelict High School and realizes that, indeed, Itomori has perished. When Miki says that there must have been some mistake, Taki attempts to prove that he is right with the memos Mitsuha left behind, but the memos all disappear before the eyes of a horrified Taki. They go to check the local library's records, and Taki finds Tessie and Sayaka's names, before finding 'Mitsuha Miyamizu' amongst the dead in the comet fragment's brutal landing to Earth.

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Taki, disheartened, has the group stay there for one more night. Miki and Tsukasa talk about Taki's plight, and she says she came to the conclusion that Taki 'met someone, and that someone changed him'. Miki notices that Taki is wearing a braided cord on his hand, and Taki realizes his final chance to meet Mitsuha - by going up the mountain to the shrine.

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Taki arrives at the shrine, and finds the 'kuchkamizake' he brought to the shrine covered in moss, proving that the Mitsuha he knew had been from three years ago, and that their timelines had been apart the whole time. Desperate, he drinks it, stating, "If time can be reversed, please give me a chance to save the town." He turns to leave, but slips and is thrown into a whole cinematic playback of Mitsuha's life - her father became close to losing himself when her mother died, and accidentally saying that he only ever cared for his wife and not the shrine, where he is told by Mitsuha's grandmother to 'get out', leaving the two young girls to be cared for by the grandmother. It also reveals that the other pieces of the comet fragment landed directly on where she was standing, presumably killing her as Taki hopelessly shouts for her to run.

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Taki gets up in Mitsuha's body back in 2013 Itomori, realising that he can save the town. He accidentally makes Yotsuha think he has 'lost it' while sobbing, and is unable to convince Mitsuha's grandmother that the comet fragment will strike the town, although, interestingly, Mitsuha's grandmother notes that she and her daughter (Mitsuha's deceased mother) all experienced the body-swapping. At the high school, Tessie and Sayaka are shocked by Mitsuha's cutting her hair, but Taki shrugs it off and tells them that they have to save the town or else everyone will die that night, yet says it loud enough for large numbers of students to hear and treat her as a nutcase. Nevertheless, the two believes Taki's story and go on to help him in his plan.

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Taki, however, is unable to convince Mitsuha's father, now the Mayor of the town, to evacuate everyone, as he believes the idea is ridiculous. Angered, Taki grabs him by the collar, calling him 'son of a-' to which the Mayor asks, "Mitsuha - no, who are you?" Taki, now rather disheartened by his failure to do his part, sulks his way back, where he encounters Yotsuha, who says that Mitsuha went to Tokyo yesterday, and is worried about her (unaware that she is talking to Taki in her body.).

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It is then revealed that, like Taki, Mitsuha attempted to meet up with Taki, also unaware that their timelines were apart. She travelled to Tokyo and retraced his steps, but was unable to find him. About to leave, she spotted him on the train, and ran after him. Finally being able to meet up with him, she is shocked to realise that the Taki from then does not recognize her, and soon enough has to leave to transfer to another train. Yet, Taki asks her for her name, to which she shouts "Mitsuha!" and throws the braided cord on her hair at him, which he catches, explaining how Taki got the cord.

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Taki suddenly remembers that if he is in her body, Mitsuha must be in his, so he runs back to the mountain to find her, having forgotten about the timeline separation. In 2016 Itomori, Mitsuha wakes up in Taki's body, staggers to the summit of the mountain and realizes that the comet fragment fell on her and killed her. She recoils in horror. Taki arrives at the summit of the mountain and starts shouting Mitsuha's name, and Mitsuha proceeds to call out Taki's name, both apparently having forgotten about the difference in timelines. Both can sense each other on the mountain, yet they cannot see each other. They stay quiet, upon which they realize it is 'kateware-doki' - twilight, and turn around and meet, having returned to their own bodies.

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Both happily reconcile with one another, although Mitsuha is disgusted that Taki drank her 'kuchikamizake', going as far as to call him a pervert. Both laugh, but only realizing that twilight is almost over then. Taki then writes on Mitsuha's hand while saying, "Mitsuha, let's write our names on each other's hands, so when we wake up, we don't forget." However, though Taki is able to finish writing, Mitsuha gets as far as one stroke before Taki is thrown back to 2016, and Mitsuha to 2013. Taki repeats Mitsuha's name over and over, yet forgets quickly. But before he loses his memory of everything, he says, "I wanted to say one thing... Wherever you are in the world, I'll come find you!" 

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Mitsuha meets up with Tessie and begins the plan. Tessie breaks into the electrical substation powering Itomori and leaves behind several timed explosives, which blow up the substation, effectively leaving everything unpowered or on their emergency generators, which allows Sayaka to use the High School's backup systems to call for an evacuation. All seems to be going well until the City Hall is able to track down and stop Sayaka's speeches for evacuation, and to which, Tessie tells Mitsuha to convince her father to help, to which she runs towards City Hall. Right after, Tessie's father and his contractor friends arrive to apprehend him, but everything stops once they all see Tiamat splitting apart.

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Mitsuha continues to run towards City Hall, all while continuously repeating Taki's name. She says she won't forget, yet, just like Taki, immediately forgets right after the 3rd repeat. Saddened, she trips and rolls down the road, but then remembers that Taki wrote his name on her hand. She opens up her palm, only to realize Taki wrote 'I love you' instead. She mutters that she can't remember his name with that, but continues running to City Hall, and is last seen marching towards her father with a new sense of determination. Then all is revealed about the comet fragment seen in the beginning, where the cutscene is completed, showing it land on Mitsuha's home, exploding out and destroying Itomori.

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Eight years (in Mitsuha's timeline but five in Taki's), it is revealed through a series of anniversary newscasts that Mitsuha persuaded her father to conduct an emergency evacuation drill across the surrounding districts, allowing most of Itomori's residents to escape in time and survive. With the two saviors unable to tell everyone about the body-swapping as they have forgotten everything, the entire incident sparked rumors and conspiracy theories about it. Taki has graduated from university and is trying to find a job, but still has lingering feelings that he is missing something important to him. He finds himself attracted to items relating to Itomori, such as magazines and people he thinks are familiar (whom he actually knew when he was in Mitsuha's body). Taki, while in a cafe, overhears Tessie and Sayaka talking about their upcoming wedding, and although he partially recognizes them, they leave before he can place a name to them. He also passes by Mitsuha, but both continue walking after glancing at one another. Taki then asks himself, "Why does the scenery of a town that no longer exists wring my heart so?"

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The next day, both wake up and head towards their respective destinations, in the first cutscenes seen after the comet at the beginning. While riding separate trains, Taki and Mitsuha are stunned to see each other when their trains parallel, where they both conclude that they were searching for someone. They get out at their next stops and try to find each other (Nandemonaiya (Movie Version)); they finally meet at the Suga Shrine staircase but then Taki seems to have forgotten what he was doing there, walking right past Mitsuha, who shows a face of despair. At the top, Taki relents, and turns around, asking Mitsuha, "Say, haven't we met before?" Mitsuha, crying tears of joy, replies, "I thought so too!" to which Taki begins crying. The movie then ends with both asking each other, "What's your name?"(in Japanese, it translates to the Japanese title of the movie, 君の名は.)