Twilight Sparkle learns that the evil Nightmare Moon will return during the upcoming Summer Sun Celebration after one thousand years of imprisonment in the moon. She tries to warn her mentor Princess Celestia, but the princess ignores her and sends her to Ponyville to check on the preparations for the celebration. There Twilight reluctantly meets Applejack, Rainbow Dash, Rarity, Fluttershy, and Pinkie Pie for the first time. At the celebration, Nightmare Moon appears in place of a missing Princess Celestia and decrees everlasting night. After Nightmare Moon decrees eternal night, Twilight Sparkle, with the addition of her new friends, ventures deep into the Everfree Forest to find the Elements of Harmony, a set of artifacts used to defeat Nightmare Moon in the past. Nightmare Moon creates obstacles to stop the six ponies, but each of Twilight's friends helps the group overcome them using their own strengths. Once they find the Elements, Nightmare Moon appears and shatters them. Twilight realizes that she and her new friends embody the Elements of Harmony—Honesty (Applejack), Kindness (Fluttershy), Laughter (Pinkie Pie), Generosity (Rarity), Loyalty (Rainbow Dash), and Magic (Twilight Sparkle)—and the six wield them to defeat Nightmare Moon, returning her to her original form as Princess Celestia's younger sister Princess Luna. Princess Celestia returns and forgives Luna, and orders Twilight to remain in Ponyville to continue studying the magic of friendship.
- Woody Woodpecker, Ttark, Thomas the Tank Engine and Percy are guest starring in this film.
- This film marks the first debut of Thomas the Tank Engine and Percy from Thomas & Friends.
- Thomas & Friends: Misty Island Rescue, Thomas & Friends: Series 13 and 14 and My Little Pony Friendship is Magic Part 1 and 2 were all released in 2010.
- The song for the credit will be "Anytime You Need A Friend" sung by The Beu Sisters from Home on the Range.
- Hades, Jafar, Ursula, The Grand Duke of Owls, Rothbart, Captain Hook, The Joker and Maleficent appeared in the bonus scene leading up to Thomas' Adventures Series.
- Ash Ketchum, Princess Azula and Henry are mentioned in this film.
- A reference to Thomas & Friends episodes - Ghost Train and Thomas, Percy and the Dragon is used.
- This is the only Winnie the Pooh/MLP:FIM crossover made by 76859Thomas. DisneyJSman will take over some of the projects until Pooh's Adventures of My Little Pony: Friendship Is Magic - Twilight's Kingdom (Full Movie) and 76859Thomas will take over again starting with Pooh's Adventures of My Little Pony: Friendship is Magic - The Cutie Map (Full Movie) onward.
- Part 1
- Part 2
- Part 3
- Part 4
- Credits/Bonus Scene