On the universal Villains ship, flux announces Buggys new position as the newest warlord of the Sea as well as the inclusion of new villains: the Deadly Six. It was after this a plan was initiated to steal a certain crown with something precious inside of it.
Zazz, Zomnom and Master Zik are sent to Equestria to Retrieve said Crown in equestria in the Crystal Empire. At the same time,a pony in a cloak sneaks into the castle, past the patrol of royal guards and into Twilight and Spike's guest room. Using unicorn magic, the cloaked pony switches Twilight's crown with a fake crown and attempts to make off with it. However, as the unicorn sneaks past Spike, he rolls over in his sleep at the last second, flipping his tail in the way. But Zazz noticed this and tried to get it back, but these two weren’t the only ones. It was desired by two others. Gengar, an ex general from the ghost kingdom Spectra as well as Misdreavus, queen of Spectra. But Zazz’s voice was too high as it awoke the young alicorn. Twilight, noticing the crown in the unicorn's saddlebag, cries "Thief!" before giving chase. Her shouts wake the other Element bearers as she passes their rooms and they quickly join the pursuit. She attempts to cut the thief off by teleporting, but the unicorn is just as skilled at teleportation as she is; uncloaked by the spell, the thief is revealed to be a mare. Twilight tackles the fleeing unicorn to the ground as they reach a chamber in the castle that houses a large mirror. During the struggle, Twilight's crown falls through the mirror. With a wicked grin and a sarcastic, insincere apology, the mystery mare untangles herself from Twilight by teleporting to the mirror and leaps through it, to Twilight and her friends' shock, as well as the others. Zazz makes a deal with the unicorn as Misdreavus retreats back to Spectra to regroup.
News of the Failed Crown heist with Zazz and Spectra in tow goes all over the world headliners, reaching the attention of the Hereos. At the time, Jexi had reached to include Hintata and Kiba, as well as two more members of Fairy Tail, Juvia and Levy, into the group. The team also welcomes back Silver and Blaze. After heading to said school, the main heroes enter in order to get info. It was here that Natsu and Happy where the first to encounter a humanized Twilight Sparkle and her dog Spike. The two become fast friends as they work together to help her get the crown.
Meanwhile, Spectra was sending its own armed forces, the Six Ghostly Pillars, in order to derail the heroes as well as trying to take back the crown. Gajeel, wanting to take the fight to them, tries to fight the Pillars and the thief singlehandedley. However, this is put on hold when they Encounter Air man and Quick man of Gospel. Using a strange device, they sent him and his group going through random universes in order to buy time for some strange purpose.
Back at CHS, Twilight grows more accustomed to her human body and closely observes the inhabitants of the strange new world she's in. As she passes by faces both new and familiar to her, she listens in on a conversation between two girls: one is being considerably cruel and verbally abusive to the other. Before Twilight could even raise a finger to defend the target of this bully, Natsu beats her to the punch, literally. He punches a locker and scares off the mean girl. After the shy girl introduces herself as Fluttershy, she tells them that they should go to the principal. Upon going, they learn the crown is a prize for becoming princess of the Fall Formal. So after signing up, they started a campaign in order to make Twilight win and triumph over Sunset. Meanwhile, Coffagregus, former Dark Crew member, is sent to the first universe that Gajeel's group arrives to to defeat them. However, misunderestimating their abilities, he is defeated by chopper. At the second one, they arrive in a futuristic world where they encounter Rotom, who keeps Gajeel on his toes as he warped from appliance to appliance before running out and being beaten to a plasma pulp. After which, the scientists of that world give them a device to travel back, but not before Rotom slips into Odd’s cell phone to wait for his chance at a counter attack.
After a huge media bomb, Twilights rep was in shambles as the human version of her friends argued. But Twilight had enough and decided to reconnect all of them. After doing so and going to the ship to spend the night, a song was born in order to create pep and perkiness as well as instill faith in this girl. At the same time, Gajeel tries his hand at retaliating against both Sunset Shimmer and Spectra himself, Juvia and Odd trying to stop him. Chandelure intervenes, expressing his familiarity to Odd as a member of Darkrai’s gang. Juvia thoroughly thrashes him with her water magic, but realizes too late that Chandelure brought backup in the form of Dusknoir. Sanji then ran in after this and battled against the ghost himself. After a flurry of ghost attacks and kicks, the ghost was defeated and they were free to return on home.
The next day, after a night of dealing with the final pillar named Aegislash, the song was performed live as everyone loved it. But this caused Sunset and Zazz to spice things up as they trashed the gym and framed Twilight for it. But a man named Flash Sentry exposed the frame up but the dance would be held off to tomorrow, leaving Twilight in a panic.
Acting fast at a local store, Jexi switches Ranma to girl form to have her go in and protect Twilight. But at this same time, Gospel’s agents Quick Man and Air Man cornered Sonic and Wendy in the shopping district in hopes of being rid of them for good. Sonic finally bested Quick Man while Air man Crashed into the store with Wendy just as Pinkie revealed the held secrets of Twilight and the heroes based on “a hunch”. Mega Man Scans Air mans weapon and with some help from the girls, Air man was cornered and beaten by Wendy, as he undersestimated her abilities as a Sky Dragon Slayer.
The Night of the Gala Finally comes. With no other option having all Six pillars defeated, Misdreavus Orders Spectra to commence an all out invasion just as Sunset steals the Crown for Flux and Zazz. However, the Mega stone inside the crown was wtiches with the Real Element of Magic. Gengar had the stone, and it just happened to be his. Using it, Gengar Mega Evolved in hopes of conquering Spectra and becoming king. But he was cut off by Hinata, so he decided to take her out first before assuming the throne. If that wasnt enough, Spectra was knocking on CHS door and Flux had finally revealed his most destructive Plan yet, himself. Fusing with Kyurem and two robots with Reshiram and Zekrom’s powers. He had become a horrible monstrosity known as Ultimate Flux. CHS became a Massive battle ground with Jexi trying to clash with Flux’s new form. But this form proved to be powerful for even Jexi to defeat as he was left bleeding and near death. It was at this moment that Twilight and her friends leapt into action. Using the real Element of Magic, twilight and company ponied up and empowered Jexi with the strength of all six magic elements and allowed Jexi to use a mode called Grand Mode. With this new overflowing amount of aura, Jexi brutally beat down Flux and his attacks. With a final barrage of fists, Flux’s body broke in two as they were sent into two different universes entirely. One just so happened to be the Kingdom hearts universe, the other was the Cosmic Circus.
After the battles were over and Sunset reformed of her evil ways, Twilight bid them all farewell as she returned home. But this didn’t last long as Twilight and her friends from the horse world met with the heroes in order to study other worlds. And at the center of it all was Rotom, who was trapped in Odd’s phone after failing to get out for his revenge. He spent whatever time was left playing mahjong on his phone.