As another year begins at Yuigaoka Girls' High School, ushering in a fresh batch of students, the school idol club Liella! is excited to expand their membership. However, Liella! is extremely popular due to the astounding talent they have continuously displayed; thus, new students lack the courage to even consider approaching the club, fearing the rigorous training that might lie ahead. Amid her worries, club leader and co-founder Kanon Shibuya meets first-year student Kinako Sakurakouji and tells her about the world of school idols. This leaves Kinako in awe, but being fairly average herself, she feels she would not be capable of matching the spirited performances of the brilliant Liella! members. Nonetheless, Kinako receives encouragement to join the group and comes to share their dream of reaching for the stars once again in the grand Love Live! Competition.

Chika Takami, a self-proclaimed normal girl, has never been involved in any clubs and lacked any notable talents. However, after a visit to Tokyo, she discovers a stage where even an ordinary girl like her could shine—the world of school idols. Inspired by the former superstar school idol group μ's, Chika is determined to start her own school idol club in her seaside hometown at Uranohoshi Girl's High School. But even before gathering any students to join the group, the aspiring school idol finds her greatest obstacle to be student council president Dia Kurosawa who stands firmly against the creation of the club. Just when it seems there is no hope, Chika meets Riko Sakurauchi, a transfer student from Otonokizaka High School, home of μ's. Somewhat shy but a talented piano player, Chika believes her to be a promising recruit, though convincing her to join is easier said than done. In spite of that, Chika chooses to charge forward and overcome the obstacles keeping her from forming a school idol group that shines as bright as the nine that came before her.

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.

Everyone has a dream they strive to achieve, and so does the musically talented Kanon Shibuya. However, due to her stage fright, Kanon fails to make it into Yuigaoka Girls' High School's music program and instead ends up in the general curriculum. Even though Kanon makes the conscious decision to quit music altogether, her classmate Tang Keke rekindles Kanon's passion for music with her own: a passion for school idols. Although Keke and Kanon try to form a school idol group, their effort meets strong objections from Ren Hazuki, the daughter of the school's director. Even so, the girls soon visit the director, who allows them to set up their school idol club under one condition—they must win first place at the Yoyogi School Idol Festival. The resilience of these aspiring idols is put to the test as they face the challenges that come their way. Throughout their journey, the girls make new friends and meet new members that join them to become the dazzling idols others can only imagine.