Junna and Senna are twin siblings that live alone. Shortly after the exams, there will be a Cherry Blossom Summer Festival at school, and Senna is excited to create memories with a relunctant Junna. Junna's homeroom teacher calls the twins over to the office to propose that they could live at the school because she is concerned about their situation. Junna doesn't recall the memories of the accident in which his parents died, but he refuses saying that he is encouraged to work hard to support his living because of Senna's existence.

Akino, the class representative of Junna's class, has decided that the theme of their activity for the Cherry Blossom Summer Festival is a haunted house. While the class groans, a student named Sana appears at Junna's class and asks him to come with her to the Helpers Club (formerly the Literature Club). It turns out that the president of the club is the most popular girl at the school, Tsubasa. Tsubasa explains the purpose of the club was to help others, and with the preparations for the Cherry Blossom Summer Festival, she believes that this is a good opportunity to get more members. She requests for Junna's help, knowing him to be very hard-working to support himself and his sister. Flattered, Junna accepts, and is given the job to collect news on the all activities in the festival. Meanwhile, Senna, who had spotted Sana dragging Junna, had eavesdropped on the conversation and is slightly bothered by it.

Junna runs into Tomo, an anti-social classmate of his who refuses to participate in the class activity. In response to this, Junna encourages her to assist and manages to help land her in a suitable role for the haunted house. Junna goes to report the Cooking Club's activity, where Tomokazu, Tomo's identical twin brother, embraces him. When Junna pushes away Tomokazu, Tomokazu's apron is accidentally soaked with soy sauce. Both Tomokazu and Senna are disappointed by this because they have to make more aprons for the rest of the club members. At the sound of trouble, Sana quickly arrives to help, but she ends up causing a fire, resulting in the arrival of the police. The officer, Yuuko, scolds the group, but also tells Junna that she had brought along his childhood friend. Junna and Senna are led outside to meet this new girl, and in turn, she addresses Junna as her older brother and hugs him. Although Junna does not remember who she is, he remembers her name, and this worries Senna.

Senna is disquieted at how much time Junna and Haruhi are spending together. Akino asks Senna for assistance because she cannot locate Junna to ask for his. She explains that the haunted house is short on decorations, and since Junna and Senna's parents are archaeologists, they might have materials that they could use. Senna leads Akino and Tomokazu to the mansion-like home she and Junna live in, and reluctantly gives Akino permission to borrow artifacts. When Tomokazu brings up the topic of club members staying at school overnight to finish constructing their club activities, Senna decides to go, despite the Cooking Club being ready. Meanwhile, Haruhi asks Junna to be her date for the Cherry Blossom Summer Festival, but Junna declines because he doesn't remember too much about her.

While making the last touches to the haunted house at night, Akino suddenly injures her leg and Junna carries her away. Haruhi becomes jealous and tries to hurt herself so Junna will carry her as well. Senna is angry that Haruhi is causing so much trouble and confronts her, and before their argument escalates, Yuuko arrives and orders Haruhi to go home. Relieved, Junna takes a break at the school roof from his work, where he sees Tomo. As the two stargaze, Tomo sagely tells Junna not to be afraid because she will always watch over him. Senna comes to the school roof, causing Junna to end his break, and she asks him if they'll be together as siblings. Junna agrees, and the two help finish the haunted house.

Senna wakes Junna up for the Cherry Blossom Summer Festival. Just as Junna promised, the two spend the entire festival together. When Haruhi shows up, she cannot locate Junna, and Junna does not hear her calling for him. When night falls, Senna tells Junna that she's happy he kept their promise, but an image of Haruhi flashes through his mind. Junna is suddenly concerned about Haruhi and his past, but Senna tries to reassure him that he doesn't need to remember everything. Just as the fireworks begin, Junna's memory suddenly flashes before his eyes, causing him to pass out.

Tsubasa invites everyone to her beach resort for summer vacation. She decides to form a beach volleyball competition, and Haruhi suggests that the winner shall have one request. Haruhi and Senna end up being stuck together as a team for the competition, but easily win, fueled by the determination to have Junna. Haruhi immediately requests that Junna should have a date with her, and hurriedly drags him away. During their date, Junna suddenly gets a flash of his mysterious dreams and ends up fainting. When Junna wakes up, Senna uses her wish from the volleyball game to request that Junna shouldn not force himself. Inwardly, Junna is still thinking about his lost memories, but is troubled with that if he does get them back, things will change.

Sana brings photos from their beach vacation to Junna and Senna's house. Senna excitedly wants to put them in photo albums immediately, and hearing this, Junna believes that if he sees the old photo albums, he may be able to recover his memory. However, Senna claims to have thrown them out by accident, but decides that they should buy one to create memories. At the bookstore, Junna notices Tomo walking by and follows her, but she mysteriously vanishes. While walking home with Senna, Junna still wonders where Tomo went. They encounter a man named Koutarou Ryuuoku, who had participated in a study with the twins' father. He tells them about a dial that their father found at an excavation site, and because the twins were present at the time, he asks them if they remembered anything from it. While Junna tries to remember, Senna tearfully exclaims that she doesn't know anything and retreats to her room.

Senna refuses to come out of her room, leaving Junna troubled as he realizes he does not know too much about her. Junna finds the dial Koutarou was talking about in his room, along with old photo albums. The photo albums have no photos of Senna, but have pictures of Haruhi instead. Shocked, Junna takes a walk outside, confused as to why this is so. He happens to meet Haruhi by chance, and the two head out to a café. Junna feels that Haruhi understands why Senna was not in the photo albums and asks her why. Haruhi sadly responds that Senna was not supposed to exist at all. Tomo appears behind Junna explains that like Junna, Senna doesn't have a past, but she does not have a future as well. As Senna emerges from her room, she notices the photo albums and realizes that Junna is coming close to knowing the truth.

Haruhi apologetically tells Junna that she cannot explain everything to him and he must be the one to choose his future, but she'll accept whatever he decides. No later, the town is suddenly engulfed in a fog, and because of this, everyone is instructed to stay home. Junna sees Tomo again and follows her down an alley, remembering that she told him that she'll watch over him. On his way, he does not see Senna, who has come to talk to Junna with the dial. Junna ends up on the school roof, and Tomo reveals herself as the Keeper of Time. She says that only Junna can decide what he want, and takes him back to the time of his childhood, on the day he was separated from his parents and Haruhi.

On the day Junna was separated by his real family, they were at an excavation site. Junna's father had showed him a dial he found and told him that the dial can grant a person's one strongest desire. Junna had wished to meet Senna, and Senna shared the same wish; as a result, the current world Junna lived in was born. In the present, Senna finds Junna at the park and reveals that when she and Junna were conceived, she died, but existed as a soul. Junna has always felt her presence, so that was why he knew of her existence. Tomo explains that since Junna and Senna's wish was granted, the dial has to take a compensation to create the world, which was the death of his parents and Haruhi living in Junna's dreams. Surprisingly, Haruhi was not supposed to exist in this new world, but because Junna had abandoned her in his dream world, she came searching for him, becoming his childhood friend in this world. Tomo informs Junna that because Haruhi and Senna cannot co-exist in the same plane, the balance between the worlds are starting to collapse, explaining the fog that has emerged in the city. She gives Junna two choices: stay with his current lifestyle with Senna or return to his old one with his parents and Haruhi.

The next morning, Senna resumes life pretending as though nothing has happened, but Junna is fed up with it. He is pressured to quickly make his decision as the world is slowly being destroyed. He is angry that his selfish wish with Senna caused his parents to die and lashes out at her for her indifferent attitude. Unmasking herself in tears, Senna says that she knew the truth from the beginning and had hidden it for so long because she didn't want Junna to be in pain. Junna expresses his desire to be with Senna together, but he wants Haruhi and his parents to be exist as his family as well. He realizes that perhaps the dial can grant his wish and goes to ask it, only to no avail. Meanwhile, Senna walks outside, where she meets Haruhi, and the two sisters walk off together.

Junna recalls that there is something more to than asking the dial one wish and forces himself to remember how it granted his wish before. Slowly, he understands that the dial will grant only wishes that more than one people share. Desperately, he looks for Senna to help him before the world is destroyed. He finds Haruhi and Senna in the park and instructs them to wish with him on the dial. In the end, Haruhi stayed as Junna's childhood friend while Senna turned out to be his future little sister.