Twilight Sparkle is surprised to learn that her older brother and Captain of the Royal Guard, Shining Armor, is to be married, and that Princess Celestia has requested her, Thomas and their friends from Ponyville to help organize the ceremony. Twilight is somewhat resentful, as she has considered Shining Armor as her "Big Brother Best Friend Forever", only coming to learn of the marriage at this late date. Twilight and her friends arrive in Canterlot, surprised to find that security has been increased, including a magic shield shell cast by Shining Armor that protects the entire city, due to an unknown threat.
Twilight berates her brother for not informing her sooner, but he apologizes, offering Twilight to be his "best mare". Shining Armor then reveals that he is marrying Twilight's favorite "foalsitter", Princess Cadance, cheering Twilight up further. However, when Twilight, Thomas and Percy first meets Cadance, she finds the bride to be cold and distant, seemingly having no memory of a special rhyme they had shared when Twilight was younger. As Twilight, Thomas and Percy observes the preparations for the ceremony, they further doubts Cadance's purpose, as the bride criticizes every aspect that their friends are planning. their friends dismiss Twilight, Thomas and Percy's claims as pressure from the upcoming ceremony mounts. They approaches Shining Armor about their concerns, but Cadance interrupts and takes her brother aside, casting an eerie spell on him that she purports to help him deal with the migraines caused by casting the shield spell around the city.
During the wedding rehearsal the next day, Twilight, Thomas and Percy barges in and decries Cadance as a fraud. Princess Celestia, Shining Armor, and their friends refuse to believe Twilight, Thomas and Percy's outrageous claims and shun them, leaving some sheepish Twilight, Thomas and Percy alone with Cadance. When They tries to apologize to her, Cadance reveals her evil side, casting a spell around Twilight, Thomas and Percy which transports Them underground. They finds themselfs in the long-forgotten crystal caves beneath Canterlot. An image of Cadance appears and taunts them, explaining that the marriage will continue without Twilight, Thomas and Percy's interference. Using Twilight's magic to shatter a crystal wall, they finds another Cadance waiting there, but the mare is bruised and battered. Twilight attacks her, but the weary winged unicorn proves that she is the real Cadance by demonstrating their shared rhyme from their youth. Cadance explains she was abducted by the impostor in the castle to marry Shining Armor herself. The four then work together to escape the caves and try to stop the wedding. Meanwhile, the fake Cadance revels in her victory, secretly plotting against Shining Armor and the others.
Just before the ceremony is completed, Thomas, Percy, Twilight and Cadance arrive to expose the deception. The impostor is forced to reveal her true form as Queen Chrysalis, ruler of the insect-like Changelings that can take on the form of any other being, thus vindicating Twilight Sparkle. Chrysalis has been usurping Shining Armor's power, weakening the shield to allow her Changeling army to invade Canterlot and take over Equestria, desiring to feed her armies off the love spread throughout the land. Princess Celestia attempts to stop her but is overpowered. Celestia implores Twilight and her friends to recover the Elements of Harmony to stop Chrysalis. Though they are able to fight through one troop of Changelings and make their way to the vault where the Elements are kept, they soon become outnumbered, surrounded and returned to the Queen as her captives. With no further resistance, Chrysalis declares her victory complete. Twilight uses the distraction to free Cadance so she may be with Shining Armor. Cadance's magic is able to break Chrysalis's spell on the groom, and with Cadance's love and magic, Shining Armor is able to recast the shield at full strength, physically expelling Chrysalis and her army from Canterlot to parts unknown.
Shining Armor, Princess Celestia, Thomas' friends and Twilight's friends apologize for doubting Twilight, Thomas and Percy, restoring their friendships. Princess Celestia commends Twilight Sparkle, Thomas and Percy for it was their instincts and conviction to them that ultimately saved the day. The wedding ceremony is quickly rescheduled, with Twilight eagerly overseeing preparations for a much happier and profoundly appreciative Cadance. Shining Armor and Princess Cadance are married, and an ensuing celebration occurs. During the ceremony and the reception, Twilight's lingering anxiety of losing touch with her brother is put to rest when Shining confesses that he persuaded Cadance to accept his proposal when he mentioned she would gain Twilight as a sister-in-law. Furthermore, just before the couple departs for their honeymoon, Shining thanks his sister for all she has done and the siblings reaffirm their love.
- Twilight Sparkle and her friends joined Thomas and his friends at the end of the film.
- Queen Chrysalis will get her revenge on Thomas, Twilight Sparkle and their friends in Thomas and Twilight Sparkle Goes to FernGully: The Last Rainforest.