On a very auspicious summer day, first year middle school student Hajime Yasaka was making a small, prank bomb for his school's "research project," and from its appearance it looked very much like an actual piece of strawberry. However inside the cherry bomb, it was filled with a large variety and amount of hot spices to be exploded once lit. Planning to put in on a strawberry cake and giving it to a classmate whom he did not get along with, Yasaka did not keep an eye on the strawberry bomb and the fuse was lit...

Yasaka Hajime came to the countryside to spend his summer holiday at his grandfather's house. After losing his way, he decided to take a break at a local coffee shop. There upon his arrival, he met Arashi, an older girl who was waitressing there, and was completely taken aback by her. Casually, he took a seat next to another local student, Kamigano Jun, and started talking to him about how wonderful Arashi is. Unbeknownst to Hajime, a figure with a scary face hidden behind sunglasses entered. Calling himself a private investigator, he informed them what he was looking for and then kidnapped Arashi...

Hajime and Arashi are flashed back to a world of the past, and Arashi still cannot believe that she is a ghost. Now, even though weird things are happening at work, all Arashi could do was think about what had recently happened. In the meantime, Hajime advises Jun that there it's strange that a freeloader has all of a sudden appeared and that they should keep a close eye on her, as Arashi becomes increasingly more immersed in her thoughts about earlier...

Knowing Arashi's secret and power, Hajime swears to keep it a secret, even though Arashi still doesn't believe that she's a ghost. One day, Hajime and crew decided to take some photos of this black-haired girl to be the lead in an independent movie with the help of some other students. Hajime and Jun go along with Arashi to a photo shop, and after examining an old wartime photo they discover it's a photo of Arashi, Kaya and another blond haired girl in the photo...

Sixty years ago, Kaya and Arashi were friends. She, like Arashi, has the ability to travel in time, coming to the present day. Hajime watches on as they are delighted and overflowing with excitement upon meeting again, in the same coffee house and waitress. However, Jun's shenanigans put Hajime in somewhat of a foul mood...

It seems as if girls always give Jun a cold shoulder or look whenever he gets close to them. Kaya provides little sympathy to Jun's plight, however she takes his hand and the next moment they are flashing back into time to 1945 (20th year in the Showa period). However, upon doing this, Jun must reveal and come face to face with a secret he's been hiding...

Kaya questions Jun and asks her whether or not she should keep up this masquerade of pretending to be a boy. In the meantime, Arashi and Hajime create some make-shift baseball gear. With all his might, Hajime hurls a ball towards Arashi, who nails it right out of the park...and breaks the weather vane above the coffee house. The weather vane, we later learn is from the prewar days, which brings back a lot of memories to Arashi and Kaya...

On their way back from buying a bunch of watermelon, Hajime and Jun decide to take a break at a nearby Shinto shrine. They spot a vending machine but only have enough money to buy one drink. Hajime suggests that they share it, however, Jun thinks that it would be like having an indirect kiss with him and refuses. Hajime gets the wrong idea and tries to force Jun to drink it, causing them to tumble down the stairs. They both get up without injury, but now they're in each other's bodies...

At the Ark Coffee Shop, the owner makes a special request to everyone. She asks them to travel back into time and bring back non-expired mackerel sushi so that she can eat it. Kaya strongly opposes to such a ridiculous request, while Jun states that if you have the ability to go back you can essentially do anything. This causes a huge debate on the ethics of time travel and changing history and if they were to jump back to an altered reality...

As their work is coming to an end, Arashi and Hajime run into Yamazaki Kanako. Kanako suddenly stabs Arashi's chest with her hand, causing her power to drain out. As Hajime is about to leap in to save her, he realizes that there's a crossbow pointed directly at him. Unable to take it as Kanako progressively weakens Arashi, Hajime - throwing caution to the wind - tries to attack Kanako...and she pulls the crossbow trigger. The arrow fires off barely missing Hajime. With little options left, in steps the man with the sunglasses...

In an attempt to save Arashi after she has her powers sucked up, Hajime and the man with the sunglasses creep into Kanako's residence. However, they could not get past Kanako's watchful eye as they fell under her attacks. While avoiding Kanako's attacks and knives, Hajime comes into contact with Yayoi and both are sent back in time to the middle of the war. They touch down on a hill on the outskirts of town, where at that time, Yayoi first met Kanako. As they approached US aircrafts, attacks commenced...

As Arashi starts to become more conscious, Kanako and Yayoi are must try even harder to maintain their presence and restore their energy to stay alive. However, they are fading as Arashi is gaining more energy. Kanako and Yayoi apologize for trying to take away Arashi's energy, and accept the punishments associated with such an act. However, Arashi, Kaya, Jun and Hajime join hands and find a way to divide the power they have to maintaining Kanako and Yayoi...but will it work...

A particular summer day, when Arashi is finally revived back, Hajime must find a solution to his cherry bomb, summer school project. However, on the way to the Ark, Arashi decides to change the name of the bomb to "Cutie Cherry Chan" bomb. Embarrassed by the name, Hajime implicitly opposes it, however Arashi has her way in the end and changes the name. Upon arrival to the Ark, they place the "Cutie Cherry Chan" on a small plate, satisfied with the way it looks. Hearing a female's voice calling out "Akagi Keiichiro," Hajime turns to where the voice came from and comes face to face with...

One day, everyone gathers at Cafe "Hako-bune", where Arashi and Hajime are working, and they discuss about the summer tradition. They end up planning to go to the beach, and Hajime is overjoyed because he will be able to see Arashi in her swim suit. Arashi, Kaya, Yayoi, Kanako are all having fun choosing swimsuits from Master's collection. But Jun, misunderstood as a boy, is having a hard time trying to keep his cover. The following day, they go to the beach in Yamashiro's car. Drawing men's attention, playing with the creatures, each one of them enjoys their summer.

After having fun at the beach, they came to an inn. They enjoyed themselves by going to saunas, outdoor hot springs, and playing mahjong. With Arashi's "kindness," Jun ends up sharing a room with Hajime. To keep her secret, Jun ends up buying men's underwear, and avoiding the bath. But in the end, Jun gets caught by Hajime and gets dragged to the bath. Arashi and Kaya save Jun. With Arashi's proposal, they end up doing a courage test. Arashi and Jun coincidentally pair up. Jun asks Arashi how she feels about Hajime.

Sucked of his life essence on a daily basis by Yayoi and Kanako, Sunglasses is somewhat groggy. Arashi proposes that only one of them use him as a source of energy supply, so Yayoi tries to find someone compatible with her from today's customers at Hakobune. Since Yayoi is shy with men, she struggles to respond back to them. With his dog, Yamashiro arrives at the café. Everyone at Hakobune urges Yayoi to go talk to Yamashiro, but, panicking, Yayoi runs away.

One day in the pouring rain, Yayoi and Hajime take the day off from work at the cafe and go over to Jun's house where Kaya is staying. Jun finds out that Hajime is coming over and panics to conceal her secret. In the midst of her panicking, Jun ends up wearing a wedding dress. Jun finally finishes hiding her underwear and such, though she forgets to hide the family portrait at the front door. As she dashes to the front door to get the portrait, the door opens, and she falls into Hajime with her wedding dress still on...

During her shift at "Hako-bune," Kanako, all of a sudden, gets dizzy and drops the salt shaker. When Kanako borrows some glasses from Arashi, she is surrounded by a bright light, transforming her into a maid warrior. Disregarding how Kanako feels, Hajime and the others, wanting to see her transform again, try to get Kanako to wear the glasses again. All of a sudden, "Hako-bune" has turned into a cosplay party for the girls.

On a very hot day, the Master comes up with a plan to prepare cold noodles. The staff at "Hako-bune" tries to recreate the amazing cold noodles that Arashi had tried once when she was young. The girls struggle in making the noodles since Kanako and Yayoi have never tried cold noodles, and Arashi does not know the exact recipe either. When it was left up to Kaya, she ended up making noodles topped with shaved ice. On the other hand, Arashi ends up creating a Neapolitan. It takes a turn for the worse when they start running the noodles in the rain gutter.

The Master panics, not knowing where she put the ceramic bowl. According to the Master, the bowl that had a bounty of one million yen at "Hako-bune" was gone all of a sudden. Arashi and the others go to search for the bowl using their time leap powers. When they arrive in the past, they find the master just wearing an apron and running around with the bowl. In the end, the master remembers that she had given the bowl to Yayoi for safe keeping, though Yayoi forgets where she placed the bowl.

On a hot day when mirages are appearing, Hajime and the others are searching for the remote control for the air conditioner. After they search through "Hako-bune," they find a pile of remote controls and start testing them. The one for the air conditioning is nowhere to be found, and it gets hotter and more uncomfortable. As it gets hotter, Kaya notices that Arashi is acting funny, and she becomes scared of her. As the number of remotes to test dwindles, Arashi can no longer bear the heat and goes crazy.

Hajime and Arashi are hanging out having fun. As Jun observes this, she refers back to the time when she talked to Arashi at the grave site. Jun remembers that Arashi tells her: "I will be gone once summer ends.” Arashi gets asked out on a date by Yamashiro in the meantime. Trusting in their "bond,” Hajime is not fazed by this. Jun believes that Hajime is too carefree about this situation. Thinking that Hajime does not know that time with Arashi is limited, she tells him that he will only be able to be with Arashi in the summer.

Arashi rejecting Hajime might have caused the two to not to be able to connect anymore. With Hajime being in a rut, Yayoi explains to him that it might have been the age difference that caused a misunderstanding between the two. Coming up with the idea that if both of them were the same age, they may be able to understand each other better, Hajime, Yayoi, Kanako, and Sunglasses time travel to when Arashi was 13 years old. Once they arrive in the past, Hajime and the others are overwhelmed by the mansion that Arashi lives in.

One morning when Jun woke up, her body was that of a grown woman. Arashi was the only one that noticed right away, though none of the others knew who she was. To get out of an awkward moment, she tells the others she is the older sister of Jun, by the name of Ryoko. When approaching Kaya to tell her the truth, Jun learns that they are planning a surprise birthday party for her. Jun ends up helping the preparations for the party. While helping the preparations, Hajime compliments on how beautiful she is, but Jun gets annoyed as the older Jun is being compared to the younger Jun.

Arashi was asked by manga illustrator, Anamori, to act out a kissing scene that will inspire her to draw the scene. First, Kaya was chosen to be her partner for the scene, but the scene failed because Kaya’s breath had the smell of gyoza. Yaoi and Kanako followed, but they were not able to successfully act out the scene either. Hajime and Jun tried to act out the scene, but this was stopped by Arashi. The place turned into chaos as Sunglasses and Yamashiro were called out to do a kissing scene.

For some reason Kaya was laying on the counter face down. Arashi suspected Hajime of doing something to Kaya seeing that she glared at Hajime every time she picked her face up. Arashi asked Hajime if anything happened, though Hajime does not recall doing anything. Kaya was actually trying to find a moment to get back at Hajime for making her drink the “Cutie Cherry Fruit Juice.” Kaya starts making something with the Kiwis that Sunglasses brought in, but Hajime and Arashi follow in taking strange actions.