Thomas and Twilight Sparkle's Adventures of X-Men: Apocalypse

Thomas and Twilight Sparkle's Adventures of X-Men: Apocalypse is the ninth upcoming Thomas/MLP/X-Men crossover made by Hiatt Grey. And is a sequel to Thomas and Twilight Sparkle meet Deadpool.

Plot
En Sabah Nur, a powerful mutant believed to be the first of his kind, rules ancient Egypt until he is betrayed by his worshippers, who entomb him alive. His four lieutenants die preserving him. Awakening in 1983, he believes humanity has lost its way without his presence. Aiming to destroy and remake the world, he recruits Cairo pickpocket Ororo Munroe, who can control the weather, and upgrades her power.

Meanwhile, Belle is using her Force powers to lift up some rocks and throw them at trees and uses her lightsaber to cut near by bamboo. Then she senses something nearby, it was a holocron. And it was very unique and she gets to open it up, which was a huge mistake a green spirit come out of it and enters in her body! And then Queen Chrysalis appears and tells her that the Changelings are dying, and that she will defend them. Belle says she will and calls her "master", as she opens her eyes fully green.

In East Berlin, shape-shifting mutant Raven investigates an underground fight club and discovers mutant champion Angel, who possesses a pair of large feathered wings on his back, and Kurt Wagner, who can teleport. Raven rescues Kurt and employs the services of black marketeer Caliban to transport him to America. En Sabah Nur recruits Caliban's enforcer, Psylocke, who leads him to Angel. En Sabah Nur enhances both their powers, transforming Angel's wings into metal.

Alex Summers discovers that his younger brother Scott is manifesting a mutation for shooting optic beams. Alex takes Scott to Professor Charles Xavier's educational institute in Westchester County, New York, hoping that Xavier and Hank McCoywill teach him to control his abilities. Scott meets the telepathic and telekinetic Jean Grey, and the two develop an attraction. Raven brings Kurt to the institute. En Sabah Nur's powers cause disturbances around the world, leading Xavier and Alex to consult with CIA agent Moira MacTaggert, who has been researching the legend of Nur.

In Communist Poland, the metal-controlling mutant Erik Lehnsherr lives with his wife and their young daughter, Nina. He uses his powers to save a coworker, prompting the militia to capture him. When they murder Erik's family, he retaliates by executing them. En Sabah Nur later approaches the devastated Erik and takes him to Auschwitz, where Erik's power first manifested. Erik destroys the camp and joins him.

En Sabah Nur remotely accesses Cerebro, a brainwave-amplifying device Xavier uses to locate mutants. Through it, he forces the telepathic Xavier to make the global superpowers launch their entire nuclear arsenals into space to prevent interference with En Sabah Nur's plan. He and his new lieutenants arrive at the mansion and kidnap Xavier. Attempting to stop them, Alex accidentally causes an explosion that destroys the mansion. Peter Maximoff, having learned that he is Erik's son and hoping that Xavier can help to find him, arrives just in time; he uses his super-speed to evacuate the students before the explosion destroys the building, but Alex is presumed dead. Colonel William Stryker's forces subsequently capture Hank, Raven, Peter, and Moira, and take them to a military facility for interrogation. Scott, Jean and Kurt follow covertly, and liberate their comrades using Stryker's mind-controlled and brainwashed experiment Weapon X, whose memories Jean partially restores.

At En Sabah Nur's behest, Erik uses his powers to control the Earth's magnetic poles, causing death and destruction across the planet. En Sabah Nur plans to transfer his consciousness into Xavier's body, and use Xavier's power to enslave every person on earth. Xavier secretly sends a telepathic distress call to Jean, and the others travel to Cairo to battle Apocalypse (En Sabah Nur) and his horsemen. They rescue Xavier, but he loses his hair as the process nears completion. Angel is defeated and incapacitated in the battle. Erik and Ororo are persuaded to turn on En Sabah Nur and, with the help of Scott, they keep him occupied physically while Xavier fights him telepathically in the astral plane. Finally, Xavier encourages Jean to unleash the full extent of her powers, incinerating En Sabah Nur, killing him for good. And soon, Cadance manages to free Belle from the spirits from Queen Chrysalis' ancestors, as she is killed by Shining Armor. In the ensuing chaos, Psylocke, Alter, Samantha, and Slate flee.

Xavier and Moira rekindle their relationship. Erik and Jean help reconstruct the school, but Erik refuses Xavier's offer to stay and help teach. Peter decides not to tell Erik yet that he is Erik's son. Hank and Raven train new X-Men recruits Scott, Jean, Ororo, Kurt and Peter.

In a post-credits scene, men in suits visit the Weapon X facility to retrieve data on Stryker's mutant research, including an X-ray and a blood sample marked "Weapon X", on behalf of the Essex Corporation.

Trivia

 * Team Griffin/Eeveelution, Peter Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark Russell Ferguson, Buttercream Sunday, Mitzi, Dolphy, Knockout, Rachel, Puffer, Mighty Joe, Daylight, Jenny, Pete, Kevin, Morley, Blitzer, Belle, Dudley Puppy, Kitty Katswell, Joy, Sadness, Anger, Fear, Disgust, Judy Hopps, and Nick Wilde guest star in this film.
 * Alter, Samantha & Slate, Queen Chrysalis, and the Changelings will work for Apocalypse in this film.
 * Thomas & Friends: The Great Race, My Little Pony: Equestria Girls - Friendship Games, Zootopia, and X-Men: Apocalypse were all release in 2016.
 * The storyline continues in Thomas, Twilight, and Logan.