Jinta Yadomi begins being pestered by a girl named Meiko "Menma" Honma, who only Jinta can see her. Meika says she wants to fulfill a wish, albeit one that she can't remember, and wanted to get all her old friends together. One of those former friends, Naruko "Anaru" Anjō, drops by Jinta's house to drop off some homework, but is on bad terms with Jinta. As Meiko pesters Jinta to go to Naruko and talk about her, they both go into the city where they run into two other former friends, Chiriko "Tsuruko" Tsurumi and Atsumu "Yukiatsu" Matsuyuki, the latter of which reacts harshly when Jinta accidentally drops Meiko's name. Frustrated, Jinta runs off and leaves Meiko behind. Jinta recalls that he, Meiko and their other friends were part of a group known as the Super Peace Busters that hang out together. One day, Jinta accidentally hurt Meiko's feelings when asked if he liked her, but Meiko died in a accident before he could apologise to her. Meanwhile, Meiko visits her family's house. As Jinta decides to search for Meiko, he checks out their old treehouse where he runs into his other old friend, Tetsudō "Poppo" Hisakawa.

Jinta tells Tetsudō about his visions of Meiko, who instantly believes him. Meanwhile, Naruko ends up encountering Chiriko, though breaks into tears when Meiko is mentioned, as she blames herself for the circumstances leading to her death. Tetsudō suggests that the wish Meiko might want granted was to have a rare Nokémon video game, which Jinta buys from the game shop Naruko works at.

After being pestered by Menma, Jinta heads towards school, but changes his mind when faced with insults from Naruko's friends. He goes to see Tetsudō, who claims he saw Menma the previous night. Jinta arrives home where Menma had attempted to make muffins that Jinta's late mother used to make, though she claims she didn't go around Tetsudō's place the previous night. The next day, Tetsudō decides to hold a 'Menma Search Party' barbecue event for the others.

After Jinta keeps her from slipping in the same spot Menma died from, Naruko hints that he can probably see Menma because he loved her. Atsumu's claims of what Menma had told her differ from the real Menma's, so Jinta brings out the muffins that Menma made earlier, hoping to convey Menma's true feelings. The next day, Jinta is visited by Chiriko, who asks him to confront Atsumu about his 'fake Menma'. As the gang gets together that night, they appear to spot a Menma running around in the woods, which turns out to be Atsumu wearing a white sundress.

Atsumu blames himself for Menma's death, and Menma has Jinta tell him things that only she and Atsumu know of. Later, Chizuru explains how she caught onto his obsession with Menma. Atsumu recalls ten years ago, when he confessed to Menma shortly after Jinta ran off, only to be rejected. Meanwhile, Jinta wonders why he hasn't been so focused on fulfilling Menma's wish lately. The next day, Naruko goes to a karaoke bar with her friends, when a boy forces her to a love hotel. However she is saved by the arrival of Atsumu. On the train ride home, Atsumu asks Naruko about her feeling's for Jinta. She is conflicted whether or not she 'likes' him. Meanwhile, Tetsudō tells Jinta his theory that Menma is around because she couldn't ascend to Heaven, but this just makes her upset.

Trying to figure out Menma's wish, Jinta decides to make his long-delayed return to school. However, his return is overshadowed over rumours about Naruko having been spotted at a love hotel. As Naruko becomes noticeably upset by all the nasty gossip surrounding her, Jinta stands up for her, and both leave class right away. With Naruko troubled about her parents hearing about the news, she decides to stay at the secret base. Hoping if there are any clues to what Menma's wish might be Jinta, Naruko and Tetsudō visit Menma's house to pay their respects, where they meet her mother, who gives them Menma's diary which they agree to read the next day. When Jinta mentions the visit to Menma, she becomes upset as she wanted her mother to forget about her so that she wouldn't be sad. Jinta in turn yells at her for never thinking of herself and runs off.

Jinta, Naruko and Tetsudō look inside Menma's diary, where they find an entry about how the group wanted to make a firework to send a letter to God to help Jinta's mother, though modern laws prevent them from making one themselves. As Chiriko asks Atsumu why he didn't bring up that Menma called the others on that fateful day, he points out it was something that was to be kept secret from Jinta. Jinta's father points him towards a friend of his that can make fireworks, but it's revealed one would cost 200,000 yen to make. Jinta takes up a part time job in order to help raise the money needed to buy a firework, working at Naruko's game store one day and Tetsudō's construction site the next. When Menma hears of this, she overhears Naruko talking about the firework and sees the work Jinta is doing for her. However the next day, the gang learn that the firework maker is no longer able to make a firework for them, under orders from one of Menma's mother.

Jinta and the others visit Menma's mother to ask about the fireworks, but she refuses, showing anger and sadness towards them about how they were able to grow up instead of Menma. Afterwards, Atsumu accuses Jinta of forcing his pain onto others, to which Jinta decides to try and solve Menma's wish himself. As Jinta's multiple jobs begin to have a negative effect on his health, Naruko urges him to stop. She reveals that she felt happy when Jinta badmouthed Menma back then because she had a crush on him, later saying that if he were to grant Menma's wish, she would just disappear again. The next day, as Jinta goes with his father to visit his mother's grave, the others receive silent calls from Jinta's house phone. Jinta is later visited by Menma's brother, Satoshi, who tells him about his memories of Menma. As the others confront Jinta at the secret base about the silent calls they had received, Menma arrives and makes her presence known by writing a brand new entry in her diary and dropping it on the floor.

The gang go round to Jinta's house where witness Menma's presence first hand, though it is shown that Menma is unable to write anywhere but the secret base. Afterwards, Atsumu says they should continue their efforts, going with Chiriko the next day to beg Menma's father for permission to have the fireworks made. As work on the fireworks begin, Atsumu becomes frustrated that only Jinta can see Menma, whilst Naruko is upset that she can't compare to her. As Atsumu tries to cheer Naruko up, Chiriko overhears Atsumu mention that he would go out with Naruko. After spending the evening with Tetsudō, Menma spots a carp in the river and goes to investigate, which scares Jinta when he spots her near the river, letting out that he wants her to stay forever.

As the gang holds a party in Menma's honour in preparation for tomorrow's fireworks, Chiriko becomes cold towards Atsumu, mentioning that on that day, Menma apparently wanted to do something for Jinta. On the night of the party, Atsumu has Naruko and Tetsudō pressure Jinta into admitting his true feelings for Menma in front of everyone. As Naruko laments his answer, Chiriko reveals to her that she loves Atsumu, to which Naruko admits she loves Jinta. Jinta asks Menma if she would rather stay here so that they could be together, to which Menma responds that she plans to go on to heaven and be reincarnated. On the day of the firework launch, Satoshi comes to watch whilst Jinta has doubts of going through with it. Jinta wants to stop the firework, however, he's too late. As the firework launches, Jinta suddenly heard Menma's voice, he looked behind and saw Menma admiring the fireworks.

As the gang gets together to discuss why Menma didn't pass on, they feel that it didn't work because their feelings were selfish. As arguments brew up, Chiriko reveals that she was jealous of Naruko for hanging around Atsumu and conspired with Menma to bring the gang together that fateful day, hoping she would be able to get together with Atsumu. Tetsudo then reveals he saw what happened to Menma on that day, feeling guilty about it ever since. Though everyone bursts into tears, they soon become happy again when everyone starts laughing at Naruko's make up faux pas. Jinta tells everyone about Menma's dream to talk with everyone, so they suggest they bring Menma to the base so they can all talk together. When Jinta returns home, he finds Menma slowly starting to disappear, as her wish was to fulfil a promise made to Jinta's mother to help Jinta learn to cry. Jinta carries Menma over to the secret base where the others are waiting, but when he gets there, he loses his ability to see Menma. As the gang try to search for her, Menma uses the last of her strength to write some final messages to everyone. Jinta calls out to her, telling her that this hide and seek game would continue forever if they don't find her. He then shouted along with his friends and Menma replied to them. Not only did Jinta was able to hear her voice but his friends did so too, they all become able to see her and give their final goodbyes before she disappears. Menma cried when she heard their blessings and suddenly remember her past when Jinta made her cry while everyone blaming him for his action. Together, they shouted "we found you" and Menma completely disappear. The next day, Jinta started going to school along with Naruko while Atsumo and Chiriko grew closer together, as for Tetsudo, he continues working on his part-time job and also tries to study. The scene later changes to Jinta with his friends in the secret fort, reading Menmas final message while thinking about the flower that blooms i