Thomas' Adventures of My Little Pony: Friendship is Magic - Magical Mystery Cure is an upcoming Thomas & Friends/MLP:FIM Crossover short film to be created by 76859Thomas. It will appear on Google Drive as a double feature with Thomas' Adventures of My Little Pony: Equestria Girls in the near future.
Twilight Sparkle awakens one morning to find that her friends' cutie marks and duties around Ponyville have swapped: Rarity's creativity in doing Rainbow Dash's weather control causes havoc around town; Rainbow is completely unable to tame Fluttershy's animals, who run wild around her cottage; Fluttershy is barely able to throw Pinkie Pie's parties and cheer up the residents of Ponyville, who are now very grumpy and tetchy; Pinkie has difficulties working on Applejack's farm, where her apple trees are now bare and blackened; and Applejack's dressmaking skills are awful at best, forcing her to close Rarity's boutique. Twilight's friends are unaware of the change, believing that it is their true destiny they must follow, despite their ineptitude with their tasks.
Twilight remembers that her mentor Princess Celestia had earlier sent her the notebook of unicorn conjurer Star Swirl the Bearded (seen at the end of "The Crystal Empire"), believing that Twilight has the skill to make sense of the final, incomplete spell on the last page. However, when Twilight first read through the notes, her magic inadvertently activated the nearby Elements of Harmony, causing the five Elements borne by her friends to switch around. Realizing her mistake is responsible for her friends' condition and finding no counter-spell to fix it, Twilight goes to cry in her bedroom, blaming herself for her friends' depression and the resulting desolation of Ponyville.
Inspired by her assistant Spike's compassion, Twilight realizes that if she shows her friends their true destinies, as well as reminding each one what they mean to each other, she may be able to reverse the spell. One by one, she shows each of her friends what their true calling is, encouraging them to help each other fix things. Each friend becomes aware of her original life and regains her original cutie mark with help of her respective Element, and Ponyville is quickly restored to normal. Twilight realizes that her friendship with the other ponies is a factor that Star Swirl had not accounted for, and is able to complete the spell. Upon doing so, the Elements worn by her friends activate on their own, engulfing Twilight in a bright light and causing her to disappear.
Twilight awakens in an ethereal place where she is greeted by Princess Celestia, who congratulates her and declares Twilight is ready for a new stage in her life. Twilight undergoes a transformation and returns to Ponyville as an alicorn. Her friends are amazed and happily welcome her change, while Celestia announces that Twilight is no longer her student, but a princess who has demonstrated leadership and other positive attributes from her friends during her stay in Ponyville. Twilight becomes concerned that she has no idea what to do now as she is no longer Celestia's student, but Celestia promises that they will all help each other to learn what may come in the future. Later, Twilight is officially crowned in a grand celebration in Canterlot, and she thanks her friends for being there to help her.