In the human world parallel to Equestria, a reformed Sunset Shimmer is ostracized by most of Canterlot High School despite her efforts to atone for her past bullying. Her only friends are the counterparts of Rainbow Dash, Applejack, Pinkie Pie, Fluttershy and Rarity, who have formed a rock band called "the Rainbooms" to participate in the school's upcoming musical showcase. The five girls discover that the magic left over from Princess Twilight Sparkle's crown has given them the ability to grow pony-like ears, tails, and wings whenever they play their instruments.

Hoping to make a fresh impression, Sunset gives a school tour to three new students – Adagio Dazzle, Sonata Dusk and Aria Blaze – and informs them of the showcase, unaware that they possess magical singing voices. Calling themselves "the Dazzlings", the trio perform a song that turns the other students aggressive and competitive towards each other, convincing them to turn the friendly showcase into a Battle of the Bands. Sunset and her friends are protected from the song by their own magic, but fail to convince the bewitched Principal Celestia and Vice Principal Luna of the danger. Sunset remembers a book that magically copies whatever she writes into another kept by Princess Celestia, her former mentor in Equestria, which she uses to send a message requesting Twilight's help.

Princess Celestia's book is delivered to Twilight's castle in Ponyville. Receiving Sunset's message, Twilight deduces that the Dazzlings are banished sirens from Equestria that feed on negative emotions to fuel their singing powers for their goal of world conquest. Twilight uses the book's magic to reactivate the portal between worlds, allowing her and Spike to return to the parallel world. Twilight and the girls attempt to use the magic of their friendship to lift the Dazzlings' spell, but it takes no effect. Concluding that they must perform a musical counter-spell, the girls enter the Battle of the Bands to give Twilight time to complete the spell, though her poor songwriting proves fruitless. The Rainbooms face hostility and sabotage from the bewitched bands throughout the competition, which raises existing tensions among Twilight's friends over certain aspects of their band.

Desperate for time in the semifinal round against Trixie's band, Rainbow Dash performs an egotistical song to substitute the counter-spell and nearly transforms, which forces Sunset to ruin her performance to keep her from exposing their plan to the Dazzlings. Despite this, the Dazzlings intervene to allow the Rainbooms' advancement to the final round, goading a jealous Trixie into trapping the Rainbooms beneath the stage to take their place. Isolated for hours, Twilight's friends finally snap and enter a heated argument, allowing the Dazzlings to absorb their magic. Sunset, realizing that their constant infighting is interfering with Twilight's spell, convinces the girls to resolve their differences, while Twilight reasons that simply playing together as friends will make the counter-spell work.

Spike rescues the girls with assistance from DJ Pon-3, a student whose headphone music protects her from the Dazzlings' spell. DJ Pon-3 provides a sound system that the Rainbooms use to engage the Dazzlings in a musical battle. Overwhelmed by the Dazzlings' projected siren forms, the Rainbooms are joined by Sunset, who assumes her own pony-like form; with her help, the Rainbooms are able to destroy the pendants that provide the Dazzlings with their singing abilities, rendering the trio tone-deaf. Returning to its harmonious state, the school drives the powerless Dazzlings away and praises the Rainbooms. Twilight and Spike return to Equestria, while Sunset finds acceptance from the rest of the school and uses Princess Celestia's book to remain in contact with Twilight.

In a post-credits scene, the alternative world's counterpart of Twilight studies the outflux of magical activity around Canterlot High School.