During a small time apart, Hope was going to school as CHS before receiving a letter that his old friends were returning. As soon as they did, he learned of the cooking guild that challenged Sanji as well as Natsu’s huge bill placed on him by the school. This was also around the same time a special competition was being held. The Friendship Games.
Hope goes to CHS to relay the news just as Sunset appears regarding one of Rainbow’s texts of an emergency. However, the only "emergency" is that Rainbow has a broken guitar string, much to her friends' frustration. Hope relays the news as the situation softens up, as the girls head inside. Sunset prepares to use her Magic journal to write to twilight, but hope stops her considering she's in the middle of a mission back home. Just then, a bus stops in front of the school, and a teenage girl in a hoodie steps off. She uses a scientific device and approaches the statue, appearing to be strangely interested in the portal to Equestria. Sunset notices the girl and calls out to her. The girl suddenly runs off, and Sunset gives chase. Before Sunset can catch up to the girl, she escapes on another bus. On the bus, she pulls off her hood to reveal herself as that world's version of Twilight.
In Vice Principal Luna’s office, Natsu admits that he had done some damage to the school on his last few visits. According to luna, it was more than some, as he destroyed several lockers, set a pool on fire, being technically impossible, and for an unknown reason, scared a hamster. Luna then offers Natsu a place as a seventh member in the Friendship games in exchange for dropping all bills against him, to which Natsu accepts finding out he cant use his Magic. Going to the library to relay the news, he overhears Rainbow’s assumption of the mystery Girl being from Crystal Prep. They soon learned of their rivalry and how Crystal Prep always wins every year. But Rainbow was determined to overcome them this year especially since three other schools were competing.
Later, at a pep rally in the gymnasium, Rainbow Dash with the help of the school marching band rallies and motivates the unenthusiastic students with a spirited song. At the song's climax, Rainbow Dash sprouts pony ears and wings. As they are warned not to show their magic during the course of the games, Hope also reveals that Crystal Prep is getting outside help… from a Color Fighter.
The Fighter in question was Volt, best known as the Lighting God for his mastery over the Lighting Style of Color Fighting. He was asked to come to CP for a substitute for an injured player, and on the way, Meets Sci-Twi. Together they head to Principal Cinch office. Having learned of Canterlot High's recent rise in test score averages and athletics, Cinch requests that Twilight and Volt join the Shadowbolts and compete in the Friendship Games to maintain Crystal Prep's reputation. Twilight is very reluctant about this until Cinch threatens to deny her application to Everton. She also targets Volt and attempts to blackmail him with his recent explorations. She also reveals that the Wild Game Chef, Golduck, was also there in order to compete with Sanji in a meat themed battle. Having no other choice, Twilight and Volt meet up with the students at the other buses, and at the time, also see one of the other schools competing, Class 3-E of Kugunigaoka Junior High, led by the Unkillable Teacher Target, Korosensei. He wanted Volt to try and kill him, but Volt revealed he didn’t really care for the teacher. On the bus, he and Sci-Twi meet Soursweet, Sunny Flare, Sugarcoat, Indigo Zap and Lemon Zest. Twilight Makes a fool of herself with her teammates, but Lemon Zest immediately hits off with Volt, bonding over his backstory of losing his father and wanting revenge against his assassin.
All schools arrive as the Wondercolt team gets ready for the mystery event, the last two schools being Hakoniwa and Fluxington. It turns out Flux has set up the fake school to keep him in cover for finding a powerful enough source to locate the Multiverse Tree. In the meantime, he registers Metal Man, Aqua Man, Slash Man, Wind Man, Color Man, Tengu Man and his personal assistant, Roll.
In the gymnasium, a welcoming party is held for the schools, but in light of the rivalry between Crystal Prep and CHS, no one appears to be getting along. Sunset informs her friends about what happened to the portal and immediately places blame upon the human Twilight. She tries to confront her, but a sudden confrontation with the other Shadowbolts prevents her from doing so. Meanwhile, Pinkie introduces herself to Twilight. Twilight notices that there isn't a lot of partying going on, and Pinkie enlists her help in fixing it, also getting the assistance of a reluctant Nagisa. As the teams are announced, Pinkie unleashed the party as Color Man joins in the fun. But as Pinkie unintentionally ponies up, her magic is not only taken by Sci-Twi’s Device, but Color Man starts malfunctioning. Volt immediately takes action and disabled Color Man’s systems, who is repaired by Tails.
The Next day, the first event is announced, the Academic Decathlon. All teams competed to their fullest abilities, but in the end, the only winner was Nagisa of Class 3-E. The time came for Sanjis match with Golduck, but with the meat pantry ransacked, Sanji had a great idea to sub for it. In the match, he used bacon and potatoes to substitute making a mock roast pork, which tasted about as good as a real one. After winning, they figured out that Flux and Ian were the ones who did the meaty deed but played coy and denied it.
The mystery event is finally announced the next day, the Tri-Cross Relay, an obstacle course conisting of Archery, Roller Derby, and motocross. Each team selected two members each for each part, but Natsu and Volt were paired for a tag team battle, running half the course and then switching. But as the event went on, strange rifts opened up leading to Equestria. During the final leg, when Indigo was close to victory, she turned around and went to save Rainbow and Medaka from a plant, resulting in a loss for Crystal Prep.
Cinch, motivated by flux, sees the device Sci-Twi has and is convinced to use it. As flux goes back to the Dark Cruster to prepare for the final stages, Indigo is convinced Flux isnt in the games to win. Tossing her competitive nature aside, she, Lemon and Volt Sneak onto Flux’s ship and see the horrid truth. Flux was preparing a giant robot mech suit with twin dimensional cannons to fire everywhere to open the path to the Multiverse Tree and he intended to use the magic Twilight was gathering as a power source for it. Before they could report ti, they were immediately captured. But with help from Guts Man, they escape and Indigo and Lemon gain an upgrade, a new weapon that was in development called Cross Armor.
Back at Campus, Cadance and Luna announce the final event of the Friendship Games: Capture the Flag. In the Wondercolts' corner, Sunset feels awful about what she said to Twilight. In the Shadowbolts' corner, Cinch tells her students that failure is not an option for this event. She suggests that they "fight fire with fire" and beat CHS at their own game by using their magic against them. With the threat of once again denying her Everton application ,Flux’s robots, Cinch and the Shadowbolts coerce Twilight to unleash the magic.
Giving into peer pressure, she unleashes it, going into her body to create something horrible, Midnight Sparkle. This horrified everyone, even Flux’s Robots who were regretting using an innocent girl like her. Putting the games aside, Indigo and Lemon arrive and get the remaining Shadowbolts and the robots to help save the students in trouble. Sunset, realizing what once happened to her is now happening to Twilight, tells her that magic cannot give her everything she wants and reveals that true magic comes from honesty, loyalty, laughter, generosity, and kindness. She destroys Twilight's device, returning the Rainbooms' magic and granting her an angelic alter ego with fiery wings: "Daydream Shimmer". Before Daydream and Midnight could clash in a no holds barred Magic Duel, Flux takes action and kidnapped the two, putting them in his machine as he laughed evilly as he began firing at random, hoping one of the rifts would be the doorway to the Multiverse Tree. Starlight takes action and overloads the mech with her own magic, while Korosensei removes Flux from the pilots seat. Indigo then uses her Immense strength boost from the guts armor to toss the suit into one of the rifts, making it explode in an empty space. Korosensei tossed Flux in a random one as they all closed after the main mech explodes.
Daydream and Midnight clash, and with an explosion, resets the chaos and returns everything to normal. Twilight shows deep remorse for what she did, but Sunset assures her that everyone will forgive her. A now furious Principal Cinch demands Celestia that Canterlot High forfeit the Friendship Games, threatening to take up what has happened with the school board. But everyone, including Volt, who finally breaks his silence, assures they wont believe her. As Cinch turns to leave, the Shadowbolt six announce that they will be joining the Team, on account of the Shadowbolts wanting to learn more about being a hero, and Volt joined in order to freely hunt down his fathers assassin and find peace.
But as they celebrated, this also gave birth to a new criminal syndicate: Nebula.