One night in Equestria, the scene panned out to some cavernous skull lair located in a swamp.
Inside the lair was three of Equestria's most notorious villains. One was Chrysalis the former Queen of the Changeling's, Lord Tirek the centaur who instead of looking old and pale looking was at medium strength with his black and red colors darker, and his horns sharper, and finally Cozy Glow the twisted little sociopath filly with a friendship complex.
Appearing before them was a big blue ram wearing a red harness with orbs that had runes on them. The ram spoke up, “It's good to see you are all awake for this.”
“How can anyone here sleep with Tirek snoring so much?” Chrysalis asked rhetorically.
“I do not snore!” Tirek argued.
“Ya kinda do.” Cozy replied, only for Tirek to glare at her.
“Silence!” the Ram announced, as the three shut up.
“So, Grogar, what is the big emergency at this hour of the night?” Tirek inquired.
“It had occurred to me that while there's strength in numbers for us, it can also be applied to our enemies.” Grogar began.
“What do you mean?” Cozy asked.
“Twilight Sparkle and her friends may be our main objective, but they have allies outside of this world. Allies that would surely stand in my way!”
“And who are these allies of whom you speak?” Tirek inquired.
Grogar motioned to the eyeball orb on the table that showed them the turtles fighting enemies in Equestria and in their world.
“The turtles!” Chrysalis gasped.
“Oh, the Turtle Ninjas of the other world!” Cozy remembered, before flying over to Grogar, “But you don't need to worry about them, Grogar. They're pretty easy to fool. And I should know. I tricked them along with Twilight and her friends.”
Grogar spoke up, “Really? Would the same go for the turtle, Michelangelo? Who wasn't fooled by your act, one bit!” he showed them scenes of Mikey distrusting Cozy Glow, and arguing with his friends about her, and finally him ranting and gloating right in her face upon her arrest. This of course made Cozy frown at that memory.
“Yes, it's true Cozy Glow's act didn't fool the young turtle,” Tirek confirmed, “But, luckily, no pony believed him. And from what I gathered from Princess Twilight Sparkle and her friends temporary stay in Tartarus, his brothers and friends never listen to him or take him seriously. And because of that, they still walked right into Cozy Glow's trap.” he snickered, until Grogar stomped his hoofs.
“And that is why, they might listen to him now!” Grogar paced around, “From what I've observed, those Turtles and their allies also have an annoying habit of showing up in Equestria at the worst possible times! And I have a guaranteed hunch that they'll show up in Equestria again.”
“Just what are you saying?” Chrysalis inquired.
Grogar squinted, “I'm going to bring in four more villains to strengthen our forces. Four villains you and Cozy Glow know too well.”
Chrysalis realized what he was talking about and spoke nervously, “Oh, no! Not them!”
“Yes... them!” Grogar drew a symbol on the ground and lit it up with his magic. Then a column of magic erupted from it, until it suddenly died down. When it did the group saw four anthro figures, “Welcome back, Dark Turtles!” he smirked.
The evil clones emerged onto the scene, but this time they looked different. Their color scheme was switched with their bodies all black with their manes and masks darker shades of their counterparts' colors, and they each had a dark purple gem shard embedded into their chests.
The four groaned, and stretched, before looking around, “What the? Where the heck are we?!” Dark Raph demanded.
“Well, don't look me! I don't know where we are!” Dark Leo growled, as he pushed Dark Raph away.
“Last thing I remember was being destroyed by the Tree of Harmony,” Dark Donnie admitted, while trying to think, “But I feel like we were brought back before in some other world in a different form.”
Dark Mikey spoke up, while looking himself over, “But now we're back. And we look cooler!” he laughed crazily.
“But who brought us back?” Dark Donnie wondered.
“I did!” Grogar stepped forward, “I am Grogar! I was the one who revived you.”
“Ha! Grofar!” Dark Raph laughed, “You supposed to be some kind of super powerful big bad or something?” He was suddenly surrounded by a yellow and black magical aura and lifted off the ground before being pulled right up to Grogar's face.
“It's Grogar! And I am!” he blasted Dark Raph into a wall, “I'm not some creature to be taken lightly. Understood?!”
“Loud and clear.” Dark Raph groaned, as he peeled off the wall.
Dark Leo spoke up, “So why did you bring us back?”
“For the same reason I brought all of them together...” he stepped aside to reveal Tirek, Chrysalis, and Cozy Glow.
Cozy flew over to the four and spoke joyfully, “Dark Turtles! Remember us!”
“Yes.” Dark Leo answered bitterly, while glaring at both Cozy and Chrysalis.
“Yep. Chrysalis created you from hairs and photos of the Turtles and you became her loyal servants, up until she abandoned you when her ex-partners, Shredder and Krang, were defeated by Twilight's students. Do you remember that?” the filly asked.
“Yessss!” Dark Donnie hissed, “And we also remember that you took us in only to frame us for your plan and let us get defeated by the turtles and destroyed by the Tree of Harmony!”
“In my defense, if you four had just stayed and watched Neighsay like I asked, you wouldn't have. So that one's on you.” Cozy stated only to get flicked away by Dark Donnie.
Grogar spoke to them, “But you needn't worry about that. Thanks to a former member, the Tree is no more! So there is nothing that can destroy you now.”
“Well, that's good to know.” Dark Mikey laughed.
“So why is it you got us all together?” Dark Leo asked, while crossing his arms.
“To answer you're question, I must first start at the beginning...” Magic seeped out of the runes on Grogar's harness, as he began telling the tale while his magic provided visuals.
“Thousands of moons ago, the land that would become Equestria was nothing more than fields and farmlands, until I declared myself Emperor of Equestria! My magical power was unmatched and unrivaled by any. And I gave life to the foulest of creatures, letting them run wild, taking what they wanted and destroying any who stood in their way. My reign was a glorious, fear-soaked epoch of darkness over Equestria. Until one day, a unicorn called Gusty the Great rose up and defeated me!”
“Um, if you're all powerful and whatnot, then how did this Gusty the Great defeat you?” Dark Raph inquired.
“By taking the item that contains most of my power: my Bewitching Bell! Gusty stole my bell and hid it somewhere, where no creature can get it. And without it, I was defeated and banished. And since then, I've spent a millennia gathering power and waiting for the perfect opportunity to seize control of Equestria. And watching all your humiliating defeats by Princess Twilight Sparkle and her friends! And do any of you four know why they've always bested you?”
“Because they cheat!” Dark Raph answered.
“They're annoyingly lucky!” Dark Donnie said.
“They play dirty!” Dark Mikey spat.
Dark Leo shouted at the three, “Because they work together, you morons!”
Grogar nodded and spoke to the gathered villains, “Well, at least one of you knows the true reason to your defeats. And that is precisely why I have gathered you all here. So that we can band together and use their own strategy to defeat them. And I have returned you four to life because the Ninja Turtles and their allies will undoubtedly return to Equestria. And we will need allies who know how they think.”
“So basically you brought us back so we can join you in defeating our enemies?” Dark Donnie guessed.
“Exactly,” Grogar answered, “Where one is weak, another is strong! And together, they're unstoppable.”
“And what if we don't want to join your little bad guy club?” Dark Raph asked defiantly.
“Then I shall return you four back to the darkness from which you came!” the villain threatened him, “But if that's not enough to convince you, then let me show you what happened to King Sombra, who also refused to join me!” he showed the Dark Turtles how the ponies defeated King Sombra in his orb.
After watching it, the four clones were shocked, as Dark Donnie spoke to Grogar, “ That's a... pretty solid argument.”
“But, if joining you means we get to have revenge on the Turtles and their allies for our defeat, then all I can say is, count us in!” Dark Leo answered, as the other three stood ready and willing.
Grogar smirked, “I'm glad you see it my way,” he walked around the four clones, and three villains, “With our combined forces, we shall inevitably defeat Princess Twilight Sparkle and her friends and Equestria will be ours!” he laughed maniacally as the scene fades to black, with only his glowing eyes showing.
That very night down in the turtles lair In New York, the four brothers were in their respective rooms sleeping peacefully, until their medallions glowed, and in their minds saw the Tree of Harmony projecting its astral form of Twilight Sparkle who spoke.
“Ninja Turtles!”
Suddenly the four turtles woke up gasping, before rushing out of their rooms and saw each other, “Did you guys see it too?” Leo asked.
“Depends on what you saw.” Mikey answered still in shock.
“I think it's safe to say we all had the same dream.” Donnie stated.
“That was freaky.” Raph said.
“What do you think this means, Leo?” Donnie asked.
“I'm not sure, Donnie,” Leo began before looking determined, “But one thing is perfectly clear. We need to go back to Equestria!”
“Alright, dimension road trip!” Mikey cheered, only to get slapped by Raph.
“Can we do this in the morning when we're actually awake?” Raph asked Leo.
“Plus we should inform the others about this.” Donnie added.
“Alright, first thing in the morning. Get some sleep.” Leo instructed, as they returned to their rooms.
As Leo laid on his bed and gazed up at the ceiling while thinking of Princess Twilight, “Twilight, please be ok.” and with that he eventually fell asleep.