Somewhere in the Everfree forest, Twilight Sparkle’s body, which is lying in a crater caused by Tirek’s magic death ball, suddenly becomes surrounded by a swarm of Changelings. A few of them venture into the hole, prepared to finish her off, when all of a sudden, they hear a loud shrieking sound and Rainbow Dash slams into the ground, creating a sonic rainboom which blasts away the first wave.
“Keep. Your. Hooves. Off. Our. Friend!” she shouts as she uses her momentum to punch and kick at a few more changelings. Another group of them close in on Twilight when a lasso appears from out of the trees and Applejack ties them to the trunk of a tree. Then, John and Emily materialize in the middle of the second wave; John extends his metal claws and the two of them work their way around the group, decimating row after row. Fluttershy, Pinkie Pie, Jenna, and Jacob soon enter the fight, with Jacob and Jenna carrying Pinkie Pie, who is in turn firing at the Changelings with her signature party cannon and Fluttershy inadvertently helping in the battle. Even Rarity eventually helps Rainbow Dash kick away the last few of them before trotting over to the crater. John clambers into the crater and leans down to listen for a heartbeat; after a short while, his face falls.
“It’s not looking good. She’s very weak, I don’t know if she can even hear us.” Just then, Twilight’s eyes open wide and she struggles to stand up.
“Wha . . . what happened? The fight, Tirek – we have to stop Tirek!” she says, only to fall back down on her side, leaving her friends very concerned.
Just then, Spike arrives, panting and wheezing; “Twi . . light . . I . . saw the . . explosion and . . came as . . fast as I . . could!” he says between gasps for breath.
“Spike,” Twilight says as John helps out of the crater, “We . . . need to –” but she only manages to fall back on her side again.
“What happened to her? Was she in the explosion?” Spike asks, concerned for his friend.
“You could say that,” Rainbow Dash says.
John presses another button on his wing-pack which causes his wings to stand out stiff like a board. “I can carry her on my wings without doing too much more damage to her,” he says, “It’s not too far back to Ponyville, right Spike?”
“Sure, but, will she be safe?” Spike asks.
“We won’t t let anything else happen to her, even if our own lives depended on it,” Jacob says confidently. So, Rarity and Emily use their magic to lift Twilight onto John’s makeshift stretcher and together the group walks back to Ponyville. Meanwhile, the villains of Equestria reunite in Canterlot, after Queen Chrysalis and King Sombra throw the royal princesses in the castle dungeon, left to mourn over presumably losing Twilight.
“Finally, we can have our kingdoms now. I call Canterlot!” Chrysalis squeals with delight like an excited filly.
“And I shall take back my crystal slaves, and I will make them suffer!” Sombra says equally excited as Chrysalis.
“You can have those, but Twilight’s castle is mine, wherever it is,” Tirek growls. “Starlight, how would you like to have Ponyville all to yourself?” he offers.
“Ponyville, hm?” Starlight considers, “Not quite as flashy as a castle, but maybe they’ll be more welcoming than my treacherous old village. Deal,” she finally agrees, and the four villains part ways for their new empires.
A few weeks pass with Equestria under control of the villains who returned from Tartarus; King Sombra’s totalitarian authority prevents the Crystal Ponies from spreading their love over Equestria, and all the nations across Equestria feel this significant change. In Canterlot, Queen Chrysalis and her Changelings finally have an official kingdom to rule, and they make everypony’s lives miserable. Tirek settles into his new home in Twilight’s castle, while Starlight Glimmer begins to spread her dreary views of friendship across Ponyville, with only a few ponies refusing to obey. Since Twilight’s castle has been taken by Tirek, the Mane 5, John, Jacob, Jenna, and Emily take shelter in Fluttershy’s house, where they try to nurse Twilight back to health, but to no avail; she continues to grow weaker by the day. After Fluttershy tends to her one day, the Mane 5 decide to discuss their options on what to do about their situation in the den.
“I’m still not sure what’s wrong with Twilight or why she suddenly became so weak,” Fluttershy says sounding very concerned, “It’s as if Tirek took something other than her magic, but her will to fight back.”
“Well, he did throw her halfway across Equestria in a ball of his dark magic,” Applejack says bluntly, “Maybe that’s how she lost her strength.”
“Maybe, maybe not,” Jacob says, “Whatever happened, it doesn’t help us now. Tirek and his gang have every corner of Equestria covered with their rule, and if we go up against them again, we’ll be sure to fail!”
“Calm down, Jacob,” John says, “There has to be a way we can figure out what happened so we can figure out what to do now.”
“Maybe I can offer some insight,” a voice says from behind the group; they all twirl around and see former Princess Celestia standing before them, looking very battered.
“Princess Celestia!” Rarity squeals, and they all bow at once; she smiles at the group but winces with every step she takes towards them.
“Are you alright, your Highness?” Jenna asks.
“Well, our time in the dungeons has taken its toll on all of us, but that is beside the point,” Celestia replies.
“Why have you come here? How did you get here?” Applejack asks.
“I teleported while the Changelings had their backs turned,” Celestia responds, “which means I don’t have much time. What can I try to help you with?”
“Do you know why Twilight has become weak and how she doesn’t have the strength to stand?” Fluttershy asks.
“I have been thinking about that myself, and I believe it is because of the connection she shares with her Element,” Celestia replies, and is met by puzzled looks from everypony. “You all share a certain connection to your Element of Harmony, just as Twilight does with hers, which gives you all a special kind of magic” Celestia explains, “However, after all this time, Twilight’s connection has become deeper than the rest of yours because of her advancing magical abilities. When Tirek took Twilight’s magic a few weeks ago, he also stole this connection away from her, so she is left with no magic and no element, which has left her in this state. Now, if you will excuse me, I would like to see my student one last time before I have to go – or, if something worse happens before I return,” she adds, choking back a sob. “I wish you all the best of luck,” and she leaves the den. After she is gone, the friends discuss what they have just learned.
“If Twilight has no magic and no connection, then I don’t think there is anything we can do to help her,” Jacob says solemnly.
“But we have to find a way,” Pinkie Pie says, losing her usually-cheery persona, “We can’t lose her!”
“But what can we do? Unless anypony has some extra magic lying around in their pocket, then I don’t see a way for Twilight to get better,” Rainbow Dash says sounding defeated.