During her summer holiday at her grandparents house Tamai Shiina, a young and cheerful schoolgirl, meets a strange looking creature. They befriend each other and Shiina names it "Hoshimaru: The Round Star." When Shiina returns home after the summer to go back to school, she starts meeting other kids that also have befriended a strange creature like Hoshimaru. But she soon finds out that not all these creatures and their masters are as friendly as Hoshimaru.

The all-girls Kikyo Private Academy and Chidori Public High School are polar opposites. With its prestigious history, Kikyo is attended by noble young ladies from distinguished families, while Chidori is infamously full of simple-minded delinquents. It is no surprise that their students clash with their differences. Having a tall stature and fierce appearance, Chidori student Rintarou Tsumugi is often avoided by others despite his gentle heart. One day, while helping out at his family's patisserie, he meets a customer who, after a brief moment, runs away from him. The next day, the customer returns to apologize to Rintarou, introducing herself as the cheerful Kaoruko Waguri. After spending time with Kaoruko, Rintarou appreciates that she does not judge him based on his appearance and looks forward to when they will meet again. However, when Rintarou discovers Kaoruko attends Kikyo, their relationship will challenge the social expectations and dynamics around them.

After inheriting the company from their parents, siblings Yuuhi and Yuamu Oudou have started to work at Ultraterrestrial Trouble Solutions, an organization that hunts aliens. Although they have never encountered aliens before, Yuuhi is desperate to meet one as he believes that an alien has stolen his important item called the "Earthdamar." One day, while searching for extraterrestrial creatures, Yuuhi and Yuamu find a strange spot in the forest where many trees have fallen, forming a scenery similar to a crop circle. As they venture further, they discover a mysterious spaceship and enter it out of curiosity. To their surprise, they come across Yudias Velgear, an alien from the Velgear Star Cluster. As it turns out, Yudias is seeking to learn about Rush Duel—a card game popular among elementary school students—as he believes that it will save his home from a long war. With the siblings agreeing to teach Yudias about Rush Duel, they eventually realize that their first contact with an alien may not be a random coincidence.

Yakumo has trained and searched for 4 years, following Pai's mysterious disappearance. However, when he finally finds her, not all is well as her memory seems to be gone. They attempt to return her memory by going to the Holy Land, birthplace of the immortal race of Sanjiyans.