The students of Canterlot High School attend a field trip to Camp Everfree, a nature camp owned by Gloriosa Daisy and her brother, Timber Spruce. During the bus ride, transfer student Twilight Sparkle has a nightmare of being overtaken by "Midnight Sparkle", a malevolent alter ego of herself produced while temporarily corrupted with magic from the alternate world of Equestria. Her friend Sunset Shimmer is supportive, relating through her own similar experience with transforming into a demon. Shortly upon arrival at the camp, Twilight develops telekinetic powers, which she worries is a sign of Midnight Sparkle's lingering presence.

That night, Timber shares a campfire story that tells of Gaea Everfree,[N 1] a forest spirit, being angered by the camp's construction and threatening to unleash a plague of natural disasters upon it; the story also mentions a trail of glittering gem dust Gaea would leave in her wake. The next day, a sailboat mysteriously crashes into a dock the campers are building to use as a fashion show runway. The terrified campers spot a trail of gem dust in the water, convincing them that Gaea is real. Later, amidst an apparent earthquake and another sighting of gem dust, Twilight's friends begin developing their own unique supernatural abilities – Rainbow Dash gains super speed, Applejack gains super strength, Rarity creates diamond-like force fields, Pinkie Pie controls explosive sprinkles, and Fluttershy communicates with animals – which they find they can only use within the camp's boundaries. Twilight believes herself to be responsible for these magical occurrences, and she prepares to run away from camp. Sunset follows Twilight into the woods and, discovering her own power of telepathic empathy, convinces her to stay.

As Timber leads them out of the forest, Sunset notices gem dust falling from his pocket and suspects him of staging Gaea's attacks. She later overhears him arguing with Gloriosa to abandon what Sunset assumes to be the camp, surmising from his longing for urban life that he means to shut the camp down by terrorizing the campers. Sunset brings Twilight and Spike with her to investigate a nearby cave kept off-limits by Timber, where they find a deposit of geodes infused with Equestrian magic. The three are confronted by Gloriosa, who reveals herself to be the true cause of the magical incidents. Sunset learns through her visions that Gloriosa, desperate to prevent businessman Filthy Rich from foreclosing the camp, has been wearing the geodes as a necklace to harness their magic in attempts at improving the campers' experience; Timber, disapproving of her reckless actions, invented the story of Gaea Everfree to cover for her.

Gloriosa adds more geodes to the necklace and is corrupted by their power, taking on an appearance resembling Gaea. She traps Twilight, Sunset and Spike in the cave, and then enshrouds the camp in brambles. The three escape and regroup with their friends, who use their powers to defend the other campers. Twilight embraces her own magic with encouragement from the other girls and, after nearly transforming into Midnight Sparkle, frees Gloriosa from the necklace's influence by splitting it apart. The pieces turn into different pendants for the girls, who gain new magical forms and restore the camp. Still faced with the camp's foreclosure, the girls realize that the geodes are the source of their new powers, and use them to organize a fundraiser ball that is held within the cave. Their plan is a success, attracting a large crowd of former campers and saving the camp. Sunset wonders about the source of the cave's magic as, unbeknownst to the campers, magic energy seeps through a crack above the portal to Equestria.

In a post-credits scene, the next day, the girls finally restore the dock, but Pinkie's sprinkles accidentally detonate and destroy it, leaving the girls and Spike in shock.