The film opens in a cozy café, where a group of teenagers is engaged in a heated argument. Their sour moods are seemingly influenced by the enchanting melodies of three teenage girls seated in a corner booth. The trio, led by Adagio Dazzle, bickers about the insufficient negative energy they have gathered to satiate their hunger for power. Suddenly, a bright flash outside captures their attention, revealing the remnants of the magical events from the first Equestria Girls film. Recognizing this phenomenon as "Equestrian Magic," Adagio, along with her companions, Sonata Dusk and Aria Blaze, resolves to track down its source and reclaim their lost abilities.
As the story unfolds, we see Canterlot High School bustling with preparations for a highly anticipated Musical Showcase. Following her recent transformation, Sunset Shimmer has been on a path of redemption, thanks to the guidance of her friends Applejack, Fluttershy, Pinkie Pie, Rainbow Dash, and Rarity. Yet, the lingering shadows of her past still haunt her, as many in the school struggle to forgive her former misdeeds.
In an unexpected turn of events during the Showcase preparations, Sunset witnesses the manifestation of pony ears and tails among her friends while they play, an inexplicable occurrence that raises alarms. Shortly thereafter, Sunset warmly welcomes three new students—Adagio, Sonata, and Aria—to Canterlot High. She becomes slightly apprehensive about their demeanor and the peculiar red pendants they wear.
Post-tour, Sunset confides in her friends, expressing her discomfort about the newcomers. As they converse, the three girls burst into the cafeteria, performing a captivating song that stirs nearly everyone into a competitive spirit for the school’s musical excellence, except for Sunset and the 'Mane 5,' who remain unaffected.
The girls suspect that something sinister is at play with the new students, but their attempts to alert Principal Celestia and Vice-Principal Luna prove futile. The Dazzlings have already enchanted the principals to transform the Musical Showcase into a Battle of the Bands, for which they’ve registered themselves as The Dazzlings.
In a state of urgency, the Mane 5 consider reaching out to Twilight Sparkle, but are dismayed to discover that the portal connecting their worlds is still sealed. It strikes Sunset that she has an old journal once used to communicate with Princess Celestia. When she writes in it, her messages magically appear in the Canterlot Library.
Meanwhile, Twilight, receiving Sunset's note in her castle, learns from her own research that the Dazzlings are no ordinary students; they are actually a malevolent trio known as "The Sirens," creatures once exiled from Equestria by Starswirl the Bearded due to their ability to thrive on negativity.
Determined to assist her friends, Twilight devises a clever plan to create a temporary portal using the journal’s magic, allowing her and Spike to journey through. Upon reuniting with her friends, Spike fills them in on the happenings since Twilight’s ascendance to the title of "Princess of Friendship" and her new residence.
On the evening of a key party, Twilight and her friends confront the Dazzlings, only to find their magical hold has strained relations among the performers. When they attempt to unite by chanting “Friendship is Magic,” nothing occurs, leading to embarrassment instead of empowerment. Adagio seizes the moment, declaring to the other groups that they seem eager to win, casting doubt on Twilight and her friends, who are not entranced by the Dazzlings’ dark magic.
As Twilight ponders the failure of their plan, Sunset hypothesizes that the Dazzlings’ power lies within their music. The group resolves that creating a musical counter-spell is crucial to counteract their influence. Twilight steps up, but with the auditions for the Battle of the Bands fast approaching, time is not on their side.
During the auditions, their efforts are disrupted by sabotaging peers, and each girl faces personal struggles impacting their performance. In a bid to uplift morale, Sunset encourages the group to relocate for practice while she keeps tabs on the Dazzlings. However, they find Sunset and exploit her insecurities, reminding her of her past mistakes.
As the auditions come to an end, the tension escalates until only the Dazzlings, the Rainbooms, and Trixie remain to compete. To assure their spot in the finals, Rainbow suggests using her song, "Awesome As I Want To Be." But while performing, she inadvertently triggers her pony features, resulting in chaos, with the school erupting in laughter at the mishap.
Just when it seems like their dreams are shattered, the girls learn they have secured a place in the finals against the formidable Dazzlings. During a rehearsing session on stage, Trixie, still harboring resentment, sets off a trapdoor, ensnaring the Rainbooms beneath the stage. As they remain trapped, tensions rise as they bicker about past grievances, feeding right into the Dazzlings’ plan.
In a moment of realization, Sunset implores her friends to halt their quarrels, recognizing that their negative energy is precisely what the Dazzlings are aiming for. With determination, the group sets aside their differences, ready to reclaim their unity and face the ultimate challenge ahead of them.