A few days before summer vacation, Natsumi Aizawa falls out with her friend, Saki Mizukoshi, when she decides to quit the tennis club. The next day, Saki reveals she is transferring schools, which upsets Natsumi. Wanting them to make up, their other friends Yuka Hanaki and Rinko Tamaki call Natsumi and Saki to a large rock at a shrine temple they used to visit in their childhood, said to grant wishes to friends who wish for the same thing. As they gather together at the rock and casually observe the sky, the rock gives off a strange magical glow and the girls soon find they are able to fly.

The day after they flew, Natsumi and Saki are still hostile towards each other. As Yuka and Rinko hang out at the rock and casually think that Natsumi and Saki are best when they're together, the rock's magic activates, causing Natsumi and Saki to become literally stuck to each other like magnets, finding themselves unable to pull away from each other. Realising this is Yuka and Rinko's doing, Natsumi and Saki cooperate with each other to chase the culprits across town. As the chase reaches its climax, Rinko mentions to Natsumi and Saki about Yuka's desire for them to make up before the two go on to stop Yuka before she runs into the ocean, only for the magic to becomes undone causing them to fall in instead. Afterwards, Natsumi and Saki apologise make up with each other. Meanwhile, one of Natsumi's brother's friends, Yuusuke, is insistant that he saw Natsumi and the others flying.

Natsumi hears from her brother Daiki about what Yūsuke claimed to have seen. As Natsumi advises the others to be careful about flying haphazardly, she and Saki make a little revenge wish to put Yuka and Rinko through what they went through the other day. As Yuka and Rinko find they are unable to get unstuck as easily as Natsumi and Saki did, Daiki and Yūsuke fall out with each other when Yūsuke takes his witch theory too far. Later, Saki runs into Yūsuke and hears about the troubles he is facing with noone believing him while Yuka and Rinko finally becoming unstuck after speaking with Daiki. In order to get Daiki and Yūsuke to make up, Saki decides she should fly once more to prove Yūsuke right. However, the rock fails to grant their wish to fly, leading the girls to realize they can't make the same wish twice. However, Natsumi manages to push Daiki to make up with Yūsuke on his own.

As Yuka learns that her cousin, Takashi Sano, who she has a crush on, has feelings for Saki, she unconsciously wishes she could be like Saki whilst sitting on the rock with Rinko. The rock's magic activates, causing Yuka to end up in Saki's body and vice versa. Yuka takes advantage of being in Saki's body to ask Takashi on a date, much to the displeasure of Saki. As the girls attempt to wish to return things back to normal, things only get worse Natsumi and Rinko end up switching bodies instead. The next day, Yuka goes with Takashi to the aquarium whilst Saki and the others follow after them. At the end of the date, Yuka comes to realise that it's Saki he likes and not her, whilst Rinko drags Yuka away before she and Takashi can kiss. As Yuka accepts the situation, everyone returns to their normal bodies before Saki sends a rejection text to Takashi.

After getting caught in the rain, Rinko ends up with a fever. With Rinko's parents going out for the day, Yuka cancels her plans to get a special poster in order to take care of Rinko. Meanwhile, Natsumi and Saki are invited by their seniors to join a tennis tournament. After Rinko recovers from her cold, Yuka catches one of her own. As the others hang out without Yuka, they recall how it was because of Rinko's odd visions and Yuka's support that the four of them became friends and begin to threat what life will be like once Saki moves. Wanting Yuka to get better, the girls prepare to make a wish on the rock only for Yuka to show up back to health. After the girls accidentally tumble down some steps together, they all become able to see the whales Rinko sees in her daydreams.

At Natsumi has her hands full with tennis, studying and looking after Daiki whilst her mother's away, Yuka, Saki and Rinko make a wish on the rock which causes Natsumi to split into two. Whilst obviously displeased with the arrangement, Natsumi starts putting good use to her doubles to get things done, with one Natsumi doing tennis practise and the other doing homework and chores. However, as the day of the doubles match comes, Natsumi notices her tennis-playing double is pushing herself too much to become stronger. As Natsumi calls to her double to come to her senses, the magic wears off and the two Natsumis become one again. Using both the training one Natsumi went through with the strategy the other learnt from Saki, Natsumi manages to put up a strong performance. Afterwards, the girl attend a festival to send off their wishes.

As the town prepares for a festival, Natsumi is at odds with Yuka for not practising for a talent competition. As Natsumi and Saki prepare for the competition and Yuka and Rinko get some last minute practise in, a sudden rainstorm appears, meaning the competition would be cancelled. Wanting the competition to go ahead, Rinko and Yuka decide to wish for the rain to stop, allowing the four to compete together and win the contest. Afterwards, they reveal it wasn't the rock they wished on, but some teru teru bozu Rinko's mother made.

As the girls debate going on a trip together before Saki moves, Natsumi suggests they go to Shimada. As the girls prepare for the trip, Saki has a nightmare about being left behind by the others. The day of the trip comes and the girls soon arrive in Tokyo and spend the night on a ferry. As Saki once again experiences the same nightmare, Natsumi tries to get her to be more honest about her feelings. Upon arriving in Shimada, Yuka almost drowns in the sea but is rescued by a lifeguard who seems agnostic towards the girls.

Upon arriving at their accomodation, the girls meet Chiharu Okiyama, the twin sister of the lifeguard from earlier, Koharu. Whilst trying to hide Saki from the neighbours in the hot springs, they inadvertently discover a wishing rock in the hotspring that causes Saki to turn invisible, unable to be seen or heard by the others. Later that night, as Natsumi talks with Yuka and Rinko about her desire to stop Saki from moving, they remind her that they'll still be friends regardless. The next day, the girls join Chiharu around the town. As they explore the hospital Saki's father will work at, Koharu becomes hostile towards them as he didn't want the doctor who used to work there to be replaced, but Chiharu assures her that she isn't the only one who misses him. As Saki comes to accept that she'll be moving here, she becomes visible again.

As the city receives a typhoon alert, the girls recall an incident when they explored a supposedly haunted hotel. With no one quite sure of what actually happened, they try using the wishing rock to remember, although it doesn't appear to work at first. However, when they get home, they find that their younger selves from four years ago are walking about. The girls follow their younger selves as they prepare to explore the haunted hotel, oblivious to the time period they are in or the approaching typhoon. As they reach the hotel, the girls find their younger selves who, believing them to be ghosts, attack them and lock them in a room. There, they realize that their younger selves are here as a result of a wish on the rock they made to see what they were like four years later. As the typhoon soon appears, the young girls are put in a dangerous situation but are rescued by their older selves.

After a bout of training, the girls soon head to Tokyo for their idol audition, where they get some last minute practice in. However, when they arrive, Yuka is suddenly overcome with nerves after witnessing the intensity of the rival competitors. Although the others assure her that she is what has made the summer vacation so far as unique as it is, Yuka is still nervous during the interview section and ends up falling down during the dance section. After failing the auditions, Yuka laments how she wanted to pass so they could stay together. After spending the rest of the day exploring Tokyo, they stop by a shrine where Saki mentions that she'll be moving on the day they return, making Natsumi wish summer vacation wouldn't end. Later in the evening, Natsumi catches a fever and mentions to Saki that she doesn't want her to leave. The next morning, the girls wake up to find they are suddenly back in Shimoda.

The girls soon realize they have gone back to the beginning of the previous day, which Yuka sees as a second chance to try and pass the audition, though it once again ends in failure. Later that day, they discover a shrine from the same family as Rinko's which has its own wishing rock and soon realize it has granted their wish for a never-ending summer vacation, which is proven when they end up looping the day over and over again. As they continue to loop, they forgo the audition and instead opt to try various other activities. After deciding they need to find a way to cancel the wish, Yuka theorizes that they may be able to escape the loop if they pass the audition. Although they manage to get through the audition, they still end up looping come midnight. Rinko then realizes they need to say goodbye to the miracles the wishing rock grants them. After spending one more day in Tokyo, the girls finally enter the next day.

Four years after the series, the four girls reunite at the wishing rock to catch up on old times and talk about their plans for the future.