X-Men in Equestria is a future project to be made by RedSilver01.
After an accidental experiment gone wrong, the X-Men are stranded in Equestria, where they make enemies and allies.
The film starts with Forge creating a teleportation device to travel to different worlds. When he inserts the final component, the machine goes haywire, and sends a huge portion of the X-Men to another world they can't find. The portal also teleports Nighlock and Nur too, because they went in after their friends.
The X-Men wake up in different parts of Equestria. Hank McCoy and Wolverine wake up in Fluttershy's cottage, Jean Grey wakes up in Pinkie Pie's home, Shadowcat wakes up in Twilight's castle, Storm wakes up in Zecora's home, Quicksilver wakes up in Rainbow Dash's house, Mystique wakes up in the Everfree Forest, and Cyclops wakes up in Sweet Apple Acres.
When the Changeling army invades with some of Equestria's most dangerous, the X-Men stand up and fight them off with their gifts. When the Diamond Dogs kidnap the Cutie Mark Crusaders, Cyclops shoots them with his optic blast. He threatens to fire another one, but Evil Trixie shoots a magic beam at him, but it stops right in front of his face, and Jean Grey steps forward and redirects it at her, and then knocks out a few Changelings with a psychic blast. In anger, Queen Crhysalis charges them, only to have her wings cut of by Wolverine, and her horn torn off by Beast. Quicksilver out speeds Gilda (Griffin) and makes her dizzy. Shadowcat arrives and Chrysalis orders her soldiers to destroy the "human", only for them to go right through her and destroy themselves. Nightcrawler arrives and easily beats The Dazzlings. Tirek order Clone Sunset Shimmer to get rid of them, but "Clone Sunset Shimmer" kicks King Sombra in the face with amazing agility, then transforms into Tirek and punches him and changes back to her real form, revealed to be Mystique. Evil Trixie demands to know what she did to their friend, and she replies that she is still alive, only she should be waking up in the Everfree Forest any minute now. Angered by this, The Dazzlings attack, only for Cyclops to shoot an optic blast at them. An all out brawl begins, with a few buildings damaged in the process. Once Tirek has enough, he starts attacking innocent ponies. At this, Apocalypse, Nighlock, and Storm show up. Apocalypse grows big and fights the evil centaur. Nighlock then asks for a weather. Storm creates a powerful whirlwind, which wasn't scheduled for the day. This starts blowing Tirek off balance, giving Nur the advantage and he send him back to Tartarus. Nighlock then changes his eye color to purple and red, which scares away the villains, and Nur goes back to normal size. The ponies throw a welcome party for the mutants, who gladly accept a meeting with the three older Alicorns. Princess Twilight Sparkle sends a letter to the three Alicorns princesses.
Celestia gets the letter, and tells her sister and niece. The Alicorn princesses travel to Ponyville and meet with the Mane 6. Nur meets with them, and escorts them to the party. When they get there, the heroes introduces themselves as the X-Men. They the go onto describe all they have faced. Then they tell them that the source of their powers is that they were born with them.
At the Changeling Hive, the Villains are mad that they got defeated by humans. Evil Trixie corrects them, saying that they are more than just humans. She explains that she felt that their powers were somehow incurable, as if they their powers were a part of them. Then The Dazzlings admit they felt the same thing when Nightcrawler defeated them, but sensed more power coming from Jean, Nighlock, and Nur, meaning they are the most powerful. They contact Bowser and he, his family, Dr. Facilier, Joker and Harley Quinn arrive. They tell them about what happened, and Joker and Harley recognize them as the X-Men. They tell them that they are more deadly than anything, because Magneto once easily destroyed everything Lex made, Nur went toe to toe with Doomsday, that Mystique easily tricked Harley by looking like Joker and th left her for dead. Frightened by this, they make plans to stop them.
Back at the Hive the next morning, the X-Men help make repairs. As they do so, Nighlock wonders what happened to Psylock, Archangel, and Magneto. Nur tells him he senses them, but he doesn't know where they are. Garble and his gang attack Canterlot, but since the X-Men are busy, the only one to deal with them is Psylock, who manages to defeat the teenagers with her two swords and her telepathy. She meets with the other X-Men and tells them she can't locate the other two either. Nighlock remembers installing a comm system into Magneto's helmet, and that either it got damaged when they arrived or he is wearing his helmet at the time. Twilight asks why does Magneto wear his helmet, and Beast explains it can keep out telepathy.
The next day, Rainbow Dash challenges Quicksilver to a race. Quicksilver accepts and they rest at a waterfall, where Gilda (Griffin) and Lightning Dust are waiting to ambush them. Before they can finish them, however, a mysterious blonde boy punches Gilda in the face. In anger, she drops him out of the sky, giving him time to unstrap. When he gets close to the ground, two large angelic wings spread out and he fights the evil Griffin in the air. When Gilda has had enough, she traps him, only for him to turn his wings into metal and escape. Archangel then challenges them both to a cage fight. Twilight, forced to set up the cage, worries that the winged X-Man could get hurt, but Nightcrawler assures her that Warren is skilled in cage fights as he was once a cage fighting campion. The fight kicks off, and Archangel fights Gilda first. After a while, he defeats her. Lightning Dust says he cheated as there is roof above the cage, and tries to remove it, only to find Nightcrawler, where he explains that's the whole point in cage fights - you have limited space. He teleports her down into the ring. They start fighting, and Applejack asks why Archangel beat her so easily. Psylock explains that their friend, while preferring to fly outside, he is quite use to limited flight space. They continue fighting, and Lightning Dust starts fighting dirty. This forces Warren to turn his wings into metal. The fight ends when he breaks one of her wings, by ramming her against the cage. The two retreat completely injured, and Nighlock puts on Heathens to celebrate Warren's victory, while everyone is surprised by Nur's cool dance moves.
The next week, the said villains cause chaos and everyone blames Discord, but Fluttershy defends him saying that he went on a space vacation. Upon hearing this, Nur confirms it by saying that he hasn't sensed the spirit of chaos since he left. The Diamond Dogs say that Nur could be a problem, but when they get home, they find that every equipment made of metal has been destroyed. The head Dog says that they just started moving on their own. Outside, in the shadows, Magneto watches. He uses his powers to take out a few guards by using chains to dislocate their legs. The next morning, the villains cause more chaos, but before King Sombra can harm an innocent foal, the Master of Magnetism crushes him with the Armour the dark unicorn wears. As the Villains look at their fallen ally's corpse, Magneto steps out of the shadows, and lifts everything that is metal. Then he scares them all away with his powers, and reunites with his friends.
Bowser, tired of the constant failure, decides to order all of them to attack. The villains attack Starlight's village. The Elements try to stop them but are overwhelmed. They proceed to destroy them, only to be intercepted by the X-Men. The Dazzlings attack Nur, but he chokes them and destroys their pendants. Magneto then proceeds to injure Bowser by manipulating the metal he wore on him, making it hard to use his fire balls. Nighlock and Jean use the power of their respected cosmic entities to banish Evil Trixie. Wolverine and Beast kill the Diamond Dogs. Archangel and Psylock fight off The FlimFlam Brothers, with Warren sacrificing one of his wings to be injured. Joker and Harley retreat, but Azula and Mistress 9 get captured.
The X-Men are thanked. Nightcrawler discovers he has the hidden ability to teleport across space and finally gets them home. Nighlock says that they should all take a vacation and everyone agrees. Apocalypse says he will look more into Equestria as he wants to know who made it.
In a mid credits scene, a giant spherical ship was watching the whole thing from a little ways away. Inside, a giant head is watching the battle on camera. The camera turns and reveals it to be none other than Galactus, who says that at least some heroes saved the peaceful world he swore upon the River Styx to never devour, the world he had created.
In a post-credits scene, Mistress 9 and Azula are seen in a cell together, when explosions are heard and gunshots. They sit back when Crossbones bursts in and breaks them out. He tells them that Bowser and Bowser Jr. hired him.
- Experiment gone wrong/Nighlock and Nur to the rescue/"Main Titles"
- The X-Men wake up in Equestria/the villains revenge
- The Villains kidnap the Crusaders/The X-Men fight back/Apocalypse banishes Tirek/scaring away the villains
- Meeting the sisters/Story time!