In the pony land of Equestria, Princess Twilight Sparkle (Tara Strong) has planned a huge celebration for a Friendship Festival in her hometown of Canterlot. But Twilight is stressing over a favor she wants to ask of the other three pony princesses. Spike the dragon (Cathy Weseluck) comes to assure Twilight that the other princesses will hear out what she's got to ask.
Twilight enters the room to speak with Princesses Celestia (Nicole Oliver), Luna (Tabitha St. Germain), and Cadance (Britt McKillip). As they are expecting beloved pony singer Songbird Serenade (Sia), Twilight wants them to move the sun and moon to get a great lighting on the show. Celestia tells Twilight that she's got the magic in her to make it a great show...which Twilight takes as a no.
Twilight's friends lend a hoof to the festivities as well. Rainbow Dash (Ashleigh Ball) goes through the clouds to get the best light. Applejack (also Ashleigh Ball) brings her family's famous apple cider. Pinkie Pie (Tabitha St. Germain) is blowing up balloon animals, but her balloon flies away as Fluttershy (also Tabitha St. Germain) is conducting a bird chorus. Rarity (Andrea Libman) is making sure everything looks lovely. Twilight comes down to join her friends and expresses her worries. Her friends come together to assure her that they got this ("We Got This Together").
Moments later, dark clouds begin to form over the town. A zeppelin descends, bringing forth creatures called Storm Guards. A little hedgehog named Grubber (Michael Pena) comes out to announce his leader, Tempest Shadow (Emily Blunt), a unicorn with a broken horn. She comes on behalf of her boss, The Storm King (Liev Schreiber), to take the power of the princesses away. Tempest uses obsidian orbs to turn the princesses to stone. Celestia tries to tell Luna to find the "queen of the hippos" before she gets frozen. Tempest thinks she's got Twilight but it was a decoy. Twilight and her friends fall through a hole in a bridge and are swept away from the city.
Tempest is contacted by Storm King, who needs the princesses' power to restore his staff. He promises to restore Tempest's horn if she succeeds. She sets out to find the ponies.
The ponies and Spike get washed up on the shore. Twilight mentions finding the Queen of the Hippos, as she thought she heard. They proceed to head toward a city called Klugetown. They meet a tall cat con artist named Capper (Taye Diggs). He takes the ponies with him to help them, gaining their trust ("I'm The Friend You Need"). Turns out Capper's actually trying to sell them to pay off a debt he owes to a gangster. When they get to Capper's house, Rarity fixes up Capper's coat, making him feel guilty for what he's trying to do. Twilight then finds a book clarifying that Celestia said to look for the Queen of the Hippogriffs on Mount Aris. A buyer then comes by to pick up the ponies, leaving Capper's deception exposed. Making things worse, Tempest shows up. The ponies run for it and hop onboard a delivery airship to escape. Tempest interrogates Capper to spill the ponies' destination, but he lies and says they are going to Black Skull Island to make up for what he did.
The ship they're on turns out to be a pirate ship, led by Captain Celaeno (Zoe Saldana). They plan to make the ponies walk the plank, but then their lunch break comes. The pirates are forced to work for Storm King, and they miss their old pirate life. Rainbow Dash convinces them that they can still be those same pirates ("Time To Be Awesome"). They decide to take the ponies to Mount Aris. Rainbow Dash makes a Sonic Rainboom, which gives away their location to Tempest. She arrives to get the ponies, but Twilight gets away with her friends in a hot-air balloon. Tempest finds out they're headed for Mount Aris and she destroys the pirate ship.
Twilight and her friends make it to Mount Aris, but it is completely empty. They hear a singing voice and follow it to a fountain where they get swallowed up by a whirlpool. They meet a seapony, Princess Skystar (Kristen Chenoweth), who gives the ponies and Spike bubble helmets to breathe underwater. Skystar guides them to her home, Seaquestria, and introduces them to her mother, Queen Novo (Uzo Aduba). They are the hippogriffs, but they used a magic pearl to help them stay underwater to hide from Storm King. Novo uses the power to turn the ponies into seaponies, and Spike into a pufferfish. However, Novo will not allow them to use the pearl to fight Storm King. Pinkie does her best to convince Novo otherwise ("One Small Thing"), and it nearly works until Twilight triggers an alarm by trying to take the pearl on her own. Novo banishes them from the kingdom.
When they reach the surface, Twilight snaps at her friends for getting in the way on the whole journey, and she causes Pinkie to cry. Although apologetic, Twilight leaves the group and is captured by Tempest.
On the ride back to Canterlot, Tempest reveals how she lost her horn as a small unicorn when a bear took it off, and how the magic she produces from it is unstable, leaving the other ponies afraid of her ("Open Up Your Eyes"). This makes Twilight feel bad for Tempest.
Spike goes to tell the ponies that Twilight's been captured. Soon, they are rejoined by Capper, Celaeno, her pirates, and Skystar to come up with a plan to rescue Twilight and stop Storm King.
Twilight is brought before Storm King so he can finally use the combined power of the princesses to power his staff and create a tornado. When Tempest asks for her horn back, Storm King says he was just using her and was never going to fulfill his promise. At the same time, Capper brings in the ponies as prisoners while the pirates are hiding in a cake. They burst out and fight the Storm Guards before running to the castle. Tempest nearly gets sucked away by the tornado, but Twilight saves her. The ponies then fight Storm King, until he loses his staff. Twilight and Storm King both try to reach the staff until the tornado pulls them away. The ponies fear Twilight is gone until she re-emerges. The ponies all hug each other. Storm King appears and tries to throw an obsidian orb at them, but Tempest jumps in the way, causing both her and Storm King to turn to stone. Storm King falls to the ground and crumbles. Twilight uses her magic to turn Tempest back to normal, as well as the princesses (and the decoy).
The city resumes their Friendship Festival with Songbird Serenade performing. Tempest shows Twilight that even without her horn, she can create something great when she uses it to make fireworks. Tempest then reveals that her true name is Fizzlepop Berrytwist. Pinkie declares that it's the best name ever.
*CUT TO THE CHASE*
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The pony land of Equestria is invaded by a broken-horned unicorn named Tempest Shadow and the guards of the Storm King. They want to use the power of the pony princesses to power Storm King's staff to control the weather. Twilight Sparkle and her friends set off to find help to stop him.
The ponies and Spike the dragon encounter many new friends along the journey before Twilight is captured by Tempest and brought back to Canterlot. Twilight learns that Tempest was shunned by the other ponies after losing her horn, which causes her to produce dark magic.
The ponies and their new allies infiltrate Canterlot to rescue Twilight and stop Storm King, who gets turned to a stone statue that shatters.
The princesses are saved, as is the whole city, and Tempest joins the ponies as a new friend.
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