Following the events of A War in Equestria, and after waiting for so many years, Apocalypse is finally ready to make his move. With help from Magneto, the Horseman of War, Storm(X-Men), the Horseman of Famine, Psylock, the Horseman of Pestilence, and new recruit BlackWarGreymon, the new Horseman of Death, he is prepared to destroy the Earth, and rebuild it in his own image, with help from the Villains. All that stands in his way are Code Red, who have taken great precautions for his move. Will they be able to save the world? Or will everything we've built fall, and from the ashes of our world, they'll build a better one?
Prologue: Fighting Apocalypse and his Horsemen/The Four Villains Retreat:
The film kicks off with Nighlock narrating about how he, Team Iron Man, and Team Cap forced Apocalypse, Magneto, Storm, and Psylock to retreat. He tells the audience how everyone thought that was the last time they would see him. And how they were wrong.
Apocalypse Awakens From his Slumber/finding his remaining Horsemen:
A few years after the War of the Apocalypse, Apocalypse awakens from a deep sleep he put on himself for when the time to strike was right. He gets up and puts on his cloak to disguise himself. He goes out and rescues Storm, who was pick pocketing some men. He tells her the time is right, and returns the Armour she wore. He then finds Psylock and gives her a new sword. Finally, they find Magneto, who is about to kill some workers that called the police on a mutant.
Hiatt Grey explains/Deadpool in Hiatt's flashback:
The heroes arrive at Hiatt Grey's beach house where he tells them how Apocalypse got his hands on him the first place. During the flashback, somehow Deadpool breaks in.
Apocalypse recruits BlackWarGreymon/Digivolve to ChaosWarGreymon:
Apocalypse and the three Horsemen find BlackWarGreymon standing on a hill overlooking the sunrise. He tells him to reach as deep as he can, and he will find that he can rot things away with his mere presence. After unleashing his full power, BlackWarGreymon digivolves to ChaosWarGreymon.
Wanda senses Apocalypse:
As Nur starts regaining his strength, Wanda is helping move some equipment for Team Cap. She is about set the box down, when she senses his presence. Knowing this could be trouble, she warns her team.
Jean Grey's Nightmare of Apocalypse:
At X-Mansion, everyone is having uneasy sleep. Charles discovers Jean is having a nightmare and sees destruction. She says it must mean that Apocalypse must have returned.
Apocalypse resurrects the fallen Villains/The Villains swear allegiance to Nur:
Apocalypse then sets to work on reviving all the fallen villains from the past five years. They thank him and immediately swear allegiance to him. The remaining villains who have survived ared reluctant at first but finally agree.
Apocalypse destroys the park:
While they were looking for Hiatt Grey, the Villains appeared and trapped the heroes. Then Apocalypse and his four Horsemen teleport onto the scene and destroy the park. Nur tells them that this is only the beginning.
Code Red calls the Avengers, X-Men, and Fantastic Four:
Realizing they need help, Nighlock brings the Avengers together, calls his fellow X-Men, and the Fantastic Four. He tells them Nur has returned, and the villains have joined him and that he now has BlackWarGreymon on his side.
Apocalypse's plot to kill Bowser and his son:
After Bowser, Mistress 9, and Bowser Jr. lead the villains who don't trust Apocalypse, the angered god-like mutant plots to kill the three in an act to get every villain on his side.
Flash and Crash Fire hear about the problem:
In their home, Flash Fire and his twin Crash Fire become aware of the problem. They don their old uniforms and go to join up with their comrades.
Apocalypse kills Bowser and Mistress 9/Bowser Jr.'s exile/Apocalypse takes over the villains:
Apocalypse puts his plot into action and kills Bowser and Mistress 9, but Bowser Jr. gets away and goes into exile. This allows Apocalypse to have every last villain join him by force.
Apocalypse gets rid of the nuclear arsenal:
While Luna is searching the night for something suspicious, Apocalypse hacks into her mind and uses her to get rid of the nuclear arsenal and then he kidnaps Princess Twivine.
Weapon X captures the Mane 6, Indominus Rex, DigiDestined, and Quicksilver:
Blaming them for the incident, William Stryker arrives and uses a sonic blast to knock everyone out. He captures the Mane 6, Indominus Rex, DigiDestined, and Quicksilver. The Avengers go to save them alongside Jean Grey, Scott Summers, Nightcrawler, and Wolverine.
Rescuing the captured Heroes:
The Avengers, Jean Grey, Scott Summers, Nightcrawler, and Wolverine arrive at the Weapon X base and sneak around. Vision draws some of the guards away alongside War Machine and Falcon. Jean Grey, Scarlet Witch, Scott Summers, Scott Lang, Nightcrawler, and Hawkeye find a room full of prisoners. As they go through the base, they fight off the guards, until they finally leave the base.
Apocalypse rebuilds his pyramid in Cairo/World Destruction:
Apocalypse then tells the villains that Cairo was meant to be the center of the universe before he was betrayed. Now it will be. He then uses his powers to rebuild his pyramid, and Magneto manipulates the magnetic field to created global destruction.
Bowser Jr. in exile/Thanos' minions recruit the former Prince:
Meanwhile, out in the desert heat, Bowser Jr. collapses from exhaustion, and is found by The Grand Duke of Owls. He reveals that his father and mother were old friends of Thanos, and Thanos is willing to recruit him.
The Heroes to the rescue:
After rescuing the captured Heroes, all the Heroes travel to Cairo to stop Apocalypse. Scott tells Mystique that not all of them can fully control their powers. Indominus tells them to not to, and embrace them.
Heroes vs the Horsemen/Deadpool vs Ernie/BlackWarGreymon's sacrifice:
The Heroes come face to face with the Horsemen, and Deadpool comes face to face with Ernie the Giant Chicken, and finally, BlackWarGreymon sacrifices himself to save everyone.
Archangel comes to his senses/helping Spider-Man save Charles Xavier:
Archangel finally comes to his senses, and guides Spider-Man to the transference. Together the two rescue Xavier from Apocalypse.
Charles confronts Tirek on the Astral plane/the final death of Tirek:
Charles decides to confront Tirek on the Astral plane, and at first he has the upper hand, until Tirek pins him down. Jean, Indominus and Taser help out and unleash the power of the Phoenix. Magneto and Storm help destroy him completely.
Every Hero vs all the Villains:
The Heroes then turn their attention to the Villains, who keep them away from Apocalypse. Eventually they retreat and leave Nur unprotected.
Nighlock vs Apocalypse/Nighlock spares Nur and takes him on as his student:
Nighlock then challenges Apocalypse to signal combat. At first Nur has the upper hand, but then all the heroes lent him their power and he defeated him. Instead of killing him, he decided to spare saying "I know you'd do it for me.". He takes him on as his student.
Flash and Crash Fire miss out on the fun:
Flash Fire and Crash Fire arrive too late. They become upset they missed out, but are treated to some nice chimichangas at El Pablo's in Starling City.
The movie ends with Canterlot being rebuilt. Nighlock, Mystique, and Cap now train the heroes for battles to come. In the epilogue, the Mad Titan Thanos goes into his vault and retrieves the Infinity Guantlet, tired of his pawns failing him.
- Prologue: Fighting Apocalypse and his Horsemen/The Four Villains Retreat
- Apocalypse Awakens From his Slumber/Finding his Remaining Horsemen
- Hiatt Grey explains/Deadpool in Hiatt's flashback
- Apocalypse recruits BlackWarGreymon/Digivolve to ChaosWarGreymon
- Wanda senses Apocalypse
- Jean Grey's Nightmare of Apocalypse
- Apocalypse resurrects the fallen Villains/The Villains swear allegiance to Nur
- Apocalypse destroys the Park
- Code Red calls the Avengers, X-Men, and Fantastic Four
- Apocalypse's plot to kill Bowser and his son
- Flash and Crash Fire hear about the problem
- Apocalypse kills Bowser and Mistress 9/Bowser Jr.'s exile/Apocalypse takes over the villains
- Apocalypse gets rid of the nuclear arsenal
- Weapon X captures the Mane 6, DigiDestined, Indominus Rex, and Quicksilver
- Rescuing the Captured Heroes
- Apocalypse rebuilds his pyramid/World Destruction
- Bowser Jr. in exile/Thanos' minions recruit the former Prince
- The Heroes to the rescue
- Heroes vs the Horsemen/Deadpool vs Ernie/BlackWarGreymon's sacrifice
- Archangel comes to his senses/helping Spider-Man save Charles Xavier
- Charles confronts Tirek on the Astral Plane/the final death of Tirek
- The Heroes vs all the Villains
- Nighlock vs Apocalypse/Nighlock spares Nur and takes him on as his student
- Flash and Crash Fire miss out on the fun
- You're Heroes/Epilogue
- Code Red (Nighlock, Major Malfunction, Taser (Phoenix form), Red Smoke, Light Ultron (Knight Mode), Air Strike, Mirage the Illusionist, Firestar, Indominus Rex (original/Phoenix form), Quicksilver (MCU), Bucky Barnes, Sauron (Marvel), Deadpool, General Maximoff, Gambit, Justice, Shark Fleet, Blue Eagle), Tino Tonitini, Ash Ketchum & Pikachu, Serena, Bonnie & Dedenne, Clemont, The DigiDestined and their Digimon (seasons 1, 2, 3, 4), The Bakugan Battle Brawlers and their Bakugan, Teenage Mutant Ninja Turtles (2012 version), Splinter (2012 version), April O'Neil (2012 version), Casey Jones (2012 version), The Mighty Mutanimals (Slash, Leatherhead, Dr. Tyler, Rockwell, Pigeon Pete), Shido Itsuka, Tohka Yatogami, Kotori Itsuka, Yoshino and Yoshinon, Reine Murasame, Origami Tobiichi, Mana Takamiya, Lor Mcquarrie, Carver Descartes,Tish Katsufrakis, Hiccup, Toothless, Astrid, Stormfly, Fishlegs, Meatlug, Snotloud, Hookfang, Ruffnut and Tuffnut, Sora and Riku, Aqua, Ventus, and Terra, Xion, Mickey Mouse, Goofy, Donald Duck, The Mixels, Mordecai and Rigby, Benson, Skips, Pops, Muscle Man, High Five Ghost, Nikolai/Thomas, D-Team and their Dinosaurs, Alpha Gang and their Dinosaurs, Mario, Luigi, Princess Peach, and Yoshi, Kim Possible, Ron Stoppable, Rufus, Sonic, Tails, and Knuckles, Amy Rose, Cream, Big, and Cheese, Shadow, Rouge, E-123 Omega, Silver and Blaze, Emerl, G-Merl, Autobots, The Eds, Dinobots, Mane 6 (humans and ponies), Cutie Mark Crusaders, Sunset Shimmer, Starlight Glimmer, Shining Armor and Princess Cadence, Princess Luna and Princess Celestia, Spyro, Cynder, and Sparx, Hiatt Grey, Goku, Vegeta, Piccolo, Gohan, Krillin, The Avengers(Captain America, Iron Man, Thor, Hulk, Hawkeye, Black Widow, War Machine, Falcon(Avengers), Vision, Scarlet Witch, Ant-Man, Black Panther, Spider-Man), X-Men(live action versions), Fantastic Four(live action versions)
Guest Stars and Cameo:
- Flash Fire, Crash Fire, Thanos
- Apocalypse, Magneto, Storm (X-Men), Psylock, BlackWarGreymon(sacrifices himself for his true friends in the end) Archangel(gets reformed), Bowser(killed by Apocalypse), Mistress 9(killed by Apocalypse) Bowser Jr. and Koopalings, Dr. Eggman, Cubot and Orbot, Metal Sonic, Nazo, Seelkadoom the Hedgehog, Team Rocket, Giovanni, Dr. Namba, Butch, Cassidy, Attila and Hun, Master Xehanort, King Nixel, Major Nixel, Nixels, The Deadly Six, Maleficent, Jafar, Pete, Natalia, Klorgbane the Destroyer, Mr. Ross, Garet Bobby Ferguson Sr, Garet Bobby Ferguson Jr, Primus, Decepticons, Dr. Drakken, Shego, Apocalymon, Devimon, Etemon, Myotismon, Dark Masters(Piedmon, MetalSeadramon, Machinedramon, Puppetmon), Lucemon, Mephistomon, Kurumi Tokisaki, The Dazzlings, Queen Chrysalis, King Sombra, Lord Tirek, Azula, Ozai, Deathstroke(only appearance/dies) will be guest stars.
- Bowser Jr. will return as a grownup in the conclusion, Infinity War where he now works for Thanos.
- Because everyone is living their normal lives, this is because Apocalypse's return erased everyone's memories of what happened and restored everything. This will all change after the events of Infinity War when it restores everything to the way it was.