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...