United they stand. Divided they fall.
The time for talking is over.
Friends will fight.
When Starlight Glimmer makes a mistake that results in innocent ponies getting hurt, Princess Celestia passes a law that goes against everything she ever taught Twilight. Now a civil war has broken out, and Twilight has been forced to lead a rebellion against the Reformed Villains Accords. With the Avengers,mX-Men and Code Red fighting alongside her, Twilight will be forced to fight some of her own friends, including Moon Dancer, whom the Winter Guard, Fantastic Four, and Suicide Squad are fighting alongside. Friendships are tested, harmony is killed off, and Twilight has been declared an enemy of Equestria, while someone the strings in the background.
The film kicks off with Moon Dancer reading over information given to her by a mysterious pony. After reading everything Starlight did wrong, and how Twilight just forgave her for it, she decides to have Princess Celestia pass a new law.
Meanwhile, in Ponyville, the town is being overun by a large pack of Timberwolves. The Mane 6 and Starlight Glimmer deal with some of the wolves and lock them in a magic cage. Starlight tries to levitate the cage into the forest, but loses her focus and accidentally drops into the Town Hall. Realizing a lot of ponies could've gotten hurt, they know there will be trouble to follow.
The next day, Celestia tells the seven that she and some of the other royals of Equestria will decide whether the new law will be passed. Wolverine shows up, and tells her that her new law is just as racist as the Mutant Registration Act, and that he won't stand for it. Moon Dancer shows up, and says that her younger sister was one of the injured, which Logan knows she's doing this for her own personal vendetta. He berates her for it, saying that he thought Equestria was built upon Friendship, Harmony, Peace, Love, Mercy, Forgiveness, etc. He then says that their creator would be ashamed of what they're doing. He storms out of the throne room, mumbling under his breath on how stupid and dumb Celestia is being.Despite Logan yelling at her, Moon Dancer refuses to forgive Starlight, even telling her to go back in time and make it so they never met, which upsets Lucas Bishop, the time traveling warrior.
Twilight Sparkle confronts Moon Dancer, but she still refuses to listen. Apocalypse teleports onto the scene, saying that Galactus made Equestria to be a peaceful world, one he swore to never devour. Vision lands on the ground, and tells her that the Mind Stone was reacting, and he sensed the Cosmic Balance was being disturbed. Scarlet Witch and Quicksilver arrive as well and remind her that despite Iron Man being the one who created the weapon that killed their mom, they forgave him. But Moon Dancer refuses to listen.
Meanwhile, Princess Celestia discusses how the look in Twilight's eye told her she felt like she betrayed her, but Princess Luna, who agrees with the Accords, tells her that Twilight needed to be more serious. Celestia knows she is right, but then Storm(X-Men), Psylock, Archangel, Major Malfunction, Shifu, Master Splinter, Magneto, Charles Xavier, and Yoda confront them both. Archangel tells Celestia that if she passes the new law, she will betray Twilight along with all of Equestria. Malfunction says that every mistake Twilight has made, is because that sometimes she worries too much. Psylock mocks Celestia and Luna, saying that Nightmare Moon was her own fault, cause she let her own sister fall down the dark path, that Discord being reformed was her idea, and she sounded pretty serious when she put that in charge of Fluttershy, that she screwed Sunset Shimmer over to the dark side herself, because she barely tried to help her, that she should've left hiding the Alicorn Amulet in the hands of the Ancient One, that she technically caused Sunburst to not use his talents, that Tirek was released because she and Luna were weak to stop it, and that everything else was he own fault. Luna asks Malfunction why he didn't do anything to stop Flash Fire from becoming evil himself, but Charles says he did more than Celestia would have done. Magneto tells her that the Major has a more strict voice than she does, and that as he Flash descended into darkness, the Cybertronian realized he may have had to expel him. Storm says that Clestia and Luna are weak to let MD have them pass the law. They leave them, but before they do, Archangel says they should've stepped away from the throne years ago. Psylock reminds the, that as he older brother, Shining Armour would vote against this alongside Cadence and Sunburst.
Meanwhile, in the streets of Canterlot, a unicorn named Ramicorn takes the memory of another pony. He has apparently a grudge against all of Equestria, and is the one who gave Moon Dancer the information.
At the conference, Malfunction has sent Nighlock to represent mutant kind. When it is decided that the law will be passed, Chief Thunderhooves storms out of the room in anger, Cadence, SA, and Sunburst leave sadly, and Nighlock just mocks every royal in the room, commenting on how they have finally managed to kill harmony in Equestria. Twilight leaves the room as well in anger, but has no idea what to do.
Three days later, two reformed criminals are captured because they would't sign. Enroute to the dungeons, Nighlock leads his most trusted warriors - Captain Plasma, his second in command, and a mutant with the ability to shoot plasma and absorb energy, General Punch, a mutant with the ability to turn into a dinosaur, whom he has left in charge of the Mutant Republic space weapon, the Star Hammer, and Clag, a mutant with the ability to turn into a wolf and the head scout. Celestia waits tirelessly for them to arrive, but Nighlock and his generals take out the guards, even Pinkie Pie, who has decided to enforce the law, and tell the two to make for the badlands and hide there.
The next morning, Pinkie and some injured guards arrive, and tell Celestia what happened. She is completely shocked about this but angry as well. She declares him an enemy of Equestria and demands he turn himself in. He refuses, and sends her a message that says that she had her chance to call off the Accords, and it's gonna blow up in her face. Twilight is inspired by this and gathers everyone who refuses the Accords. Gambit appears in the throne room and tells her that she betrayed all of Equestria. Iron Man enters as well and tells her that she just started a war.
Twilight and Nighlock recruit Discord, Trixie, Applejack, Rainbow Dash, STarlight Glimmer, Shining Armor, Princess Cadence, Sunburst, The Avengers, X-Men, and Code Red. Moon Dancer, angered by all this, together with Amanda Waller, recruits Luna, Rarity, Pinkie, Adagio Dazzle, Aria Blaze, Sonata Dusk, Sunset Shimmer, Russia's superhero team the Winter Guard, Suicide Squad, and the Fantastic Four.
Celestia orders MD and her team to bring in the rebels. A Changeling Scout, who long betrayed Queen Chrysalis, says he has managed to find one of their bases in the docks of Manehatten. The team heads there, and manages to capture Shadowcat, War Machine, and Bishop. Vision, Scarlet Witch, Apocalypse, and Quicksilver arrive, and capture Sunset, Luna, and Human Torch. They know they gotta break out their friends.
A few days later, and the Pro-Registration has designed a microchip that'll allow them to control villains who have not reformed. The Anti-Registration breaks them out, while dealing with a mind controlled Diamond Dog at the convoy. Ben Grimm, completely disgusted by this, joins the Anti-Registration, while Nighlock convinces Susan Richards and her brother Johnny Storm to switch sides as well. The team gets away while Flash Fire starts figuring out that whoever sent MD is behind all of this and goes solo to find him.
Cap and Stark discover that a building was severely damaged, but Gambit finds out it was one of Stark's. They realize it's a trap, but Team MD prevents them from leaving. Nighlock secretly hands Twilight a device that'll deactivate Moon Dancer's magic. They make their escape, while Deadpool buys them time, killing a mind controlled Garble, but he gets captured. After this, MD tells them they have 48 hours to surrender.
Seeking to avenge him, Twilight rallies the resistance to steal a jet from the airport, so they may free all reformed villains. Indominus discovers that Flash is missing and finds him on Ramicorn's trail. The two set off to find him.
Meanwhile, at the airport, Team MD confronts Twilight on the Tarmac. There, they tell her that she should surrender now. Falcon tells her they found the jet, and Hawkeye shoots an arrow that breaks off Twilight's cuffs. Apocalypse distracts the Winter Guard, while Ant-Man gets Twilight her weapon. The Avengers deal with Pinkie, the X-Men deal with the Squad, and Code Red deals with Mister Fantastic. They make their way to the jet, but Radioactive Man stops them, telling them to surrender now. This results in the two sides charging at each other and clashing. Falcon(Avengers), Hawkeye, Scarlet Witch, Ant-Man, Light Ultron, Firestar, Taser, Blue Eagle, and his partner, Blue Wing are all captured, with Radioactive Man inadvertently paralyzing Adagio.
Meanwhile, Flash and Indominus come across Nick Fury, who has recruited Ghost Rider, Maria Hill, Luke Cage, Iron Fist, Jessica Jones, and Daredevil into bringing in Ramicorn. The two young heroes join Fury willingly. They find out he has a plan to completely destroy harmony.
Before the Equestrian Avengers launch their next attack, they are joined by Superman half of the Justice League.
Nighlock and Twilight lead the resistance to free all the unregistered reformed villains and mind controlled villains. Then Team MD appear alongside Batman and the other half of the Justice League, and battle them. The strongest rebel teleport era teleport every out of there, but into the streets of Canterlot. The Four know that if innocents get hurt, they're no better than bad guys. Apocalypse helps the, evacuate the civilians of Canterlot. The two sides clash, and eventually it is between Twilight and Moon Dancer. Twilight beats down on MD, but hesitates on the final blow. She decides to surrender herself, as long as her allies are given a head start. Nighlock promises to come back for her, and Hiatt Grey gets the rebels out of Canterlot, clearly not interested in signing or rebelling. The guards agree and take her in.
Meanwhile, Fury and the Secret Warriors have tracked Ramicorn to the Dragon Lands, where Garble's gang is mourning their leader's death. Flash reminds them none of this would've happened if Celestia had listened, if Moon Dancer hadn't let her own rage get the better of her, and if Ramicorn hadn't given MD the information in the first place. They decide to join them to avenge Garble. They leave to find Ramicorn somewhere in the Dragon Lands.
Meanwhile, Twilight has been sentenced to eternal imprisonment. Nighlock sends a letter to Celestia, saying that she truly betrayed Twilight, and she has been too foolish to listen anymore. Celestia burns the letter, but for some reason, it doesn't work. She looks in the mirror to Earth and sees the one responsible - Galactus. He tells her that he warned Star Swirl that one day their rulers would turn on Equestria and start a war. He tells her that she has soiled the peaceful land of Equestria, and curses her name. The original members of Code Red break Twilight out of prison.
Back in the Dragon Lands, Ramicorn is almost done hacking the mind controlled villains. The Secret Warriors arrive, and Indominus distracts him while Flash stops the hacking and initiates the knock out sequence. The mind controlled villains are knocked out, and he deactivates the micro chips completely, and tells them through their earpieces to get a headstart. The villains do so, and the Secret Warriors bring in Ramicorn. They go into hiding while Moon Dancer finally realizes her mistake. Celestia weeps for the damage she has caused, for now Equestria is a land full of War, Hatred, and Chaos, something Discord no longer stands for.
In a mid-credits scene, The resistance is in hiding at different places such as the Xavier Institute, Major Mansion, New Avengers Facility, Stark Tower, and the Shield Helicarrier. Twilight, who is hiding with Code Red at Major Mansion with AJ and RD, thanks Nighlock for doing this.
In a post credits scene, all the fighting in Equestria is revealed to have awakened a the Dark Dragon, the evil Dragon Lord that is said to awaken when Equestria is in great chaos and war. The evil dragon sets out to wreak havoc.
- This film is based off of Captain America Civil War and the comic book titled Civil War.
- Starlight's mistake is a reference to when Scarlet Witch hurt some people on accident.
- Team Twilight Sparkle will consist of Twilight as the leader, Nighlock as the second in command, Discord, Trixie, Applejack, Rainbow Dash, Starlight Glimmer, Shining Armor, Princess Cadence, Sunburst, The Avengers, X-Men, and Code Red
- Team Moon Dancer will consist of Moon Dancer as the leader, Amanda Waller as the mission monitor and consultant, Princess Luna, Rarity, Pinkie Pie, Adagio Dazzle, Aria Blaze, Sonata Dusk, Sunset Shimmer, the Winter Guard, Suicide Squad, and Fantastic Four.
- The movie has two sides to it. Twilight's and Moon Dancer's.
- The storyline continues into Weekenders Adventures Chronicles: Legend of the 7 Original Dragon Lords.
- Moon Dancer decides to write to Celestia
- Timberwolf invasion/Starlight's mistake
- Celestia reveals the new law/Moon Dancer supports it/Wolverine yells at Moon Dancer
- Twilight, Apocalypse, Vision, Quicksilver, and Scarlet Witch confront Moon Dancer
- Storm, Psylock, Archangel, Malfunction, Charles Xavier, Magneto, Shifu, Splinter, and Yoda confront Celestia and Luna
- Ramicorn's evil plot
- The conference/the law shall be passed
- Freeing the reformed criminals/reporting to Celestia
- Assembling Team Twilight Sparkle
- Assembling Team Moon Dancer
- Street Chase/Gleaming Shield, Sunset Shimmer, and the Royal Guards capture Twilight, Nighlock, Captain America, Rainbow Dash, Light Ultron, Falcon, Applejack, Quicksilver, and Bucky
- Zemo and General Maximoff break the crew out/Escape from Canterlot
Team Twilight Sparkle
- Attack on the Manehatten base/Shadowcat, War Machine, and Bishop get captured/Vision, Scarlet Witch, Apocalypse, and Quicksilver arrive/Sunset, Luna, and Human Torch get captured
- The Mind Controlled Villains/break out at the convoy/Thing, Invisible Woman, and Human Torch switch sides/Flash Fire goes solo and leaves the Anti-Reg
Team Moon Dancer
- Siberian Overture - Captain America: Civil War