Following the closure of Uranohoshi Girls' High School, the third-year students—Dia Kurosawa, Kanan Matsuura, and Mari Ohara—have just graduated, leaving Aqours with solely the first and second-years. While searching for a new place the remaining members can use to practice, they decide to visit the new school they will soon enroll in. However, to their surprise, the building seems to be abandoned! It turns out that due to the school board's worries regarding how the freshly transferred Uranohoshi students may burden the clubs, they were instead sent to a branch school. This sets Aqours on a new goal—to prove that Uranohoshi students are serious in their clubs as well. Meanwhile, another problem arises: the third-years have unexpectedly gone missing during their graduation trip! Love Live! Sunshine!! The School Idol Movie: Over the Rainbow revolves around the remaining Aqours members as they venture out to search for their missing seniors and, at the same time, try to figure out a way to change the new school's mind.

There have been many cases of stolen songs happening among the idols in Yokohama District recently. Even super idol Marine Amagi's hit song "Kiseki no Uta" was taken away. At the request of Marine, the Milky Holmes team starts investigating the case.

Summer break has arrived, but while his other classmates are out having fun, Kimihiro Watanuki continues to work as compensation for the eccentric Yuuko in her shop. With the spirits and supernatural phenomena that bother him lessening, he pays his dues by cleaning, cooking, and doing whatever else the apparently lazy Yuuko needs. Watanuki, however, gets involved in a new predicament when Yuuko receives a mysterious invitation to a mansion whose owner seeks Yuuko's wish-granting ability. When he, Yuuko, and his classmate Shizuka Doumeki make their way to the peculiar residence, they meet others who were summoned by the same strange invitation. All of them are collectors of various unique items, drawn there by the chance to expand their collections. But as the collectors begin to disappear one by one, Watanuki and his companions must solve the mystery and put the case to rest, or find themselves in risk of danger.

It is said that fireworks can calm the souls of the dead. For Tomoya Sugisaki, Aoi Harukawa, and Ryou Kobayashi, fireworks are what allowed them to meet the Summer Ghost. Believed to be the spirit of a young woman who committed suicide, the Summer Ghost only appears in a specific area and can only be seen by those who are within arm's reach of death. Tomoya is a creative soul being crushed by his academic obligation to get into a good university. Aoi is a meek girl who is relentlessly bullied by her classmates. Ryou is a former basketball star who had to forfeit his passion following a grim diagnosis. The only thing these three have in common is their ability to see the Summer Ghost. The Summer Ghost is said to be able to answer any and all questions pertaining to death—something the three teenagers desperately want to know more about. Dissatisfied with their initial meeting, Tomoya sets out to find the Summer Ghost once again. But the more time he spends with the ghost, the more the mystery surrounding her existence unravels.