When the sun came up over Ponyville, everypony was ready to start the day. Twilight, her friends, and the ninjas were all meeting in the throne room.
“So you gave the students the day off?” Leo asked the Princess.
“Yes. We all know Shredder, Krang, and Chrysalis will be putting their plan together, and I wanna make sure the students are all safe. As well as anypony else.” Twilight explained.
“When that Technodrome surfaces, we'll be ready.” Donatello said.
“Especially since we know what we're up against.” Donnie added.
“We totally got this, yo.” Bebop said.
“Da. We can do anything when we're together.” Rocksteady put in.
“So what's the plan?” Applejack asked.
“We should all patrol around Ponyville in case there's any disturbances to keep us from going after the Technodrome.” Leo instructed.
“Agreed,” Twilight confirmed, “Everypony split up and cover every inch of the town.” And so the group broke and headed off.
Meanwhile down below in the Technodrome, Shredder, Krang, and Chrysalis stood before the Dark Turtles, Night Terror, and the Purple Nightmares.
The evil ninja spoke up, “Attention, every pony. Over the last couple of weeks, we've had multiple setbacks due to your failures to get the job done.” the henchmen frowned while feeling the urge to attack, until Krang continued.
“However, all of it is about to pay off. For once we head for the surface and open the portal to Dimension X. We will conquer this dimension together!”
“And exact revenge on all those who stood in our way.” Chrysalis finished.
“And though we've been hard on the lot of you for your failures, we honestly could not have gotten this far without your help. So once we've conquered Equestria, you will all have a place at our side.”
“Ooh, I like the sound of that.” Dark Mikey said with excitement.
“And I will put together an ever bigger gang than ever before.” Night Terror added.
Krang turned to one of the Purple Nightmares, “Put the Sombra crystals into the machine.”
“As you wish, Master Krang.” the Purple Nightmare answered, as they dropped the crystals into a compartment on the control board.
“To the surface!” Shredder declared, as the Technodrome's drill extended and started drilling a tunnel upward.
Dark Leo spoke to his brothers, “Soon, we will crush those goody turtles and prove we are the superior ones.”
“And with these medallions, we're sure to take them down.” Dark Donnie added.
“I'm just itching to try them out on those losers.” Dark Raph finished.
Back in Ponyville, the ponies and ninjas had scoped out the whole town to see everything was normal. At least as normal Ponyville can be.
“Well, nothing out of the ordinary here.” Raph said, as Pinkie popped out of a nearby barrel.
“I know.” she agreed.
“You think maybe they're still buying their time?” April wondered.
“I wouldn't be so sure.” Fugitoid feared.
“What do you mean, Professor?” Fluttershy asked.
“I'm sensing vibrations from underneath us.” Fugitoid said, as his hooves were picking up movement.
“The Technodrome is coming!” Leonardo gasped.
“And right under Ponyville?!” Rarity gasped in shock.
“We need to evacuate, and hurry!” Keno ordered.
Twilight nodded and used the Royal Canterlot voice, “Attention everypony! You are to evacuate the town and go to shelter. This is not a drill! I repeat, this is not a drill!”
Taking the Princess' words to heart, every pony in Ponyville started making a run for it to safety. When the ground started shaking some more they saw the ground open up and rising out from it was the Technodrome.
“There it is!” Mikey gasped.
“So that's the Technodrome?” Starlight asked.
“So round.” Pinkie marveled.
They saw the door of the base open up and a ramp extended from it. Coming right down was Shredder, Krang, Chrysalis, and their henchmen.
“Good morning, everypony.” Krang laughed.
“Nice day, isn't it?” Shredder asked.
“A lovely day for an invasion.” Chrysalis snickered.
“Shredder and Krang.” Leonardo squinted at the two.
“Chrysalis.” Twilight frowned at the villainess.
“If you guys have any common sense you'll take your Technodrome and leave.” Leo warned them.
“Otherwise we're gonna have to make you.” Rainbow added.
“We'd like to see you try,” Krang laughed, before speaking into a comlink, “Start the portal!”
In the Technodrome a Foot Bot pulled a switch and the giant eyeball on the base looked up and started projecting a portal in the sky.
“Oh, dear. Here they come!” Fugitoid feared.
“Here who come?” Rarity wondered.
Suddenly dropping down from the portal were the small rock monsters followed by Traag and Granitor.
“Them.” Karai answered.
“I think we might have us a problem here.” Applejack said, as the rock creatures readied themselves.
“We'll handle them all together.” Leo assured her.
“Attack!” Shredder announced, as the rock creatures went into battle along with the two rock titans.
“Get'm!” Leo ordered, and they went into battle.
The ninjas fought the smaller rock creatures with their ninja skills, while the ponies used their own strengths against them. Rocksteady charged at Traag attempting to make him fall over, but the giant rock man swapped the rhino away making him roll across the ground.
“Hang on, Rock!” Bebop jumped in and used an energy mohawk on Traag disorienting him, only for the former thief to get swatted aside by Granitor.
Night Terror fought Casey and Keno with his brute strength, while the other Purple Nightmares engaged as well, “Today is where I make you pay for getting half my gang sent to the clink.”
“When this is over we'll be sending the rest of you there.” Keno promised.
“And it'll be a life sentence.” Casey added, as the two vigilante's fought the mutated gang.
The eight turtles ponies made their way through the rock creatures before finding themselves face to face with the dark ones.
“Whoa! Who're these guys?” Michelangelo asked.
“The Dark Turtles.” Mikey answered.
“Wow. These guys sure swam at the shallow end of the gene pool.” Raphael joked.
“I'm gonna rip your mouth right off!” Dark Raph growled.
“You guys don't stand a chance against all of us.” Raph warned him.
“Oh, don't we?” Dark Donnie asked, as the medallions of the Dark Turtles glowed and started levitating above them with black markings covering their bodies before powering up into dark armored forms.
“Uh, they couldn't do that before, right?” Mikey asked.
“How is this happening?” Leo asked in shock.
“Just a little contingency Chrysalis came up with!” Dark Donnie answered.
“So whatever you can do, so can we.” Dark Leo declared, as they attacked the good turtles.
“Come on, guys!” Leo ordered, as they tapped into their own medallions and powered up.
Each of the turtles fought their dark self with their elemental powers, while the dark turtles used the same elemental powers only theirs were darker.
“How long have you been working for Chrysalis?!” Leo demanded.
“Details, details! I'd pay more attention on keeping your head on!” Dark Leo answered, as the two clashed in a fight of water and wind power.
Karai, Shini, and Fugitoid in anthro mode were attacked and shooting at several rock creatures that kept trying to attack them.
“You'd think after fighting them in the city we'd be able to handle it.” Shini said.
“Well, this time we're in another land, and fighting in different forms.” Fugitoid reminded her.
“No matter what form we're in. We're still us.” Karai said, as they kept on fighting, until Traag and Granitor closed in on the three.
Before they could attack, a shockwave of magic hit Traag making him bump into Granitor. The heroes looked over and saw Blade Swipe.
“We heard you could use some assistance.” Blade told the guys.
“Blade!” the ponies cheered.
“Who's 'we'?” Raphael asked.
Suddenly joining at Blade's side were the Pillars along with the Kiican Generals, “It's the Pillars!” Sunset gasped.
“And the Generals!” Donnie cheered.
“Don't forget about us.” came a voice, as Celestia and Luna flew down.
“Princesses!” the heroes cheered.
Celestia called out to the villains, “As the rulers of Equestria, my sister and I order you to cease this madness!”
“We've come too far to turn back now!” Chrysalis called back.
“Alright, everypony. For Equestria!” Starswirl ordered his comrades.
“Are you ready, my siblings?” Yaotl asked his siblings.
“Always.” Aguila agreed.
“Let's go!" Blade drew his sword, and the cavalry joined in the battle.
Each of the legendary ponies were overpowering the rock creatures taking the slack off some of the ponies and the ninjas.
“Dudes, the Pillars and the Kiican generals fighting together?” Mikey asked his bros, “My mind is blown!”
“Not yet it's not!” Dark Mikey called, as the two engaged in battle.
Luna flew around blasting at multiple rock creatures, until Night Terror and his gang approached her, “So our mighty empress blesses us with her presence.”
“You have the wrong pony.” Luna replied.
“Do we?” one of the Nightmares asked.
“You may be Princess Luna now, but you will always be Nightmare Moon to us.” Night Terror said.
“Your children of the night.” another Nightmare finished.
“Never!” Luna attacked them, only for the Nightmares to whip out Dimension X blasters and started shooting at her.
Luna cast a shield spell to deflect their shots, before firing back at them, destroying their blasters in the process.
As the alternate turtles made their way to Shredder, Leonardo spoke while aiming his sword at him, “Give it up, Shredder. It's all over.”
“On the contrary, you cretins. It's far from over.” Suddenly a shadow cast over everyone to reveal Krang had activated his suits molecular expander and was bigger than even the two stone generals.
“It's only beginning!” Krang laughed.
“That is one ugly Trojan Horse.” Raphael said.
Krang started stomping around and kicking the ninjas and ponies around, as more and more rock creatures kept falling through the portal, while an army of Foot Soldiers armed with blasters came down the Technodrome ramp to aid their masters.
Watching from the School of Friendship was the Young Six who could see the Technodrome and Giant Krang in the distance, “Oh, man. Our teachers and sensei's are out there risking their lives.” Silverstream said in worry.
“I know. While we're here doing nothing.” Smolder grumbled.
“Yona can't stand to just watch.” Yona said.
“So why don't we do something?” Gallus asked.
“What do you mean/' Ocellus asked.
“Gallus is right,” Sandbar agreed, “Sure we're still training, but we've come a long way since then. Our spirit quests have proven that.”
“What he said.” Gallus agreed.
“So let's go and help them!” Smolder declared.
“Yeah!” the students agreed.
“Hold it,” came a voice, as they saw Metalhead who was left behind to protect the students should anything happen, “No one is going anywhere...”
“But Metalhead, they need us.” Sandbar pleaded.
“They did so much for us, so now we wanna help them.” Ocellus said.
“We're going whether you like it or not.” Smolder added.
“We'll even fight you to help them.” Gallus put in.
“You didn't let me finish,” Metalhead replied, “No one is going anywhere without me.”
“Huh?” they asked.
“It is my job to look after the six of you, and if you were to go there without me then I cannot do my job of keeping an eye on you. So let's got together.” he gave a thumbs up.
The students smiled, “Yeah!” Sandbar cheered, as they rushed out of the room and through the school halls.
As they charged down the hall, they ran right past Cozy Glow who called, “Where are you all going?”
“To save Equestria!” they called back, much to Cozy's confusion.
Back at the fight, the good guys were on the ropes with all that was going on, “We got to stop these creatures.” Serpiente said, as she dodged some rock creatures.
“But how?” Gato asked.
“We have to take out that eye!” Donatello motioned to the Eyeball projecting the portal.
“We're on it!” Luna answered, as she and her sister flew for it, but Krang kept swatting them away like flies.
“You're not doing anything to my portal!” Krang called.
The turtles were panting, while the Dark Turtles still looked ready for some more, “Bros, if we don't find a way to turn the tides, we may be over.”
“I hate to say it, but Mikey's right.' Raph agreed.
“Allow us to turn the tides!” came a voice as Sandbar and Metalhead led the charge.
“What the?” Shredder asked, as the students engaged the rock creatures allowing the heroes to get themselves together and resume fighting.
“What're you all doing here?” Twilight asked in shock.
“We couldn't sit back and watch you all risk your lives.” Ocellus said.
“Equestria is home to all of us. And we wanna help protect it.” Smolder added.
“So let's work together!” Yona cheered.
“Because that's what being a team is all about.” Gallus put in.
“Affirmative.” Metalhead confirmed.
The group smiled seeing how much their students have learned and resumed fighting. Yona ran with Rocksteady, “Let's take out Krang legs.
“Roger that.” Rocksteady agreed, as they ram against two of Krang's robot pony legs making him lose his balance and bump into the Technodrome knocking the eyeball off.
“No the portal!” Chrysalis called, as the portal started phasing out, and started sucking the smaller rock creatures back.
“Alright!” Blade cheered.
“Now for these two.” Starswirl looked to Traag and Granitor. He along with Twilight, Sunset, and Starlight combined their magics and blasted the two soldiers to pieces that were sucked back into the portal.
“No! This can't be happening!” Shredder cried, as Applejack bucked him to the ground.
Upon getting up Shredder got a party cannon full of pies courtesy of Pinkie Pie, followed by a flying tackle of Rainbow Dash, and suddenly wrapped in fabric by Rarity who finished it with a red ribbon.
“Perfect.” Rarity smiled.
With the Rock creatures assimilated back into Dimension X, the ninjas plowed through all the Foot Soldiers, while Night Terror and the Purple Nightmares looked around.
“This is getting too heavy, boss.” a Purple Nightmare told Night Terror.
“Let's get out of here!” Night Terror ordered, as they tried to make a run for it only for Casey and Keno to fly in and knock them all out.
“Yeah!” the two vigilante's cheered.
Dark Leo growled, “I have had it! We're going to destroy you all if it's the last thing we do!” The dark turtles started glowing and took the form of dark versions of the turtles in dragon form.
The turtles themselves tapped into their medallions and transformed into dragons as well. The eight dragons engaged in an epic fight, which shocked Spike and Smolder.
“Ever seen a dragon fight like this?” Spike asked.
“Never in my life.” Smolder replied.
“The turtles could still use our help.” Twilight told everyone.
“And it is what they shall get.” Celestia answered.
So Twilight, Sunset Shimmer, Starlight, Celestia, Luna, Starswirl, Stygian, Blade, April, Yaotl, Serpiente, and Mono combined their magics and sent a blast at the Dark Turtle Dragons, as if holding them in place.
“Hurry, Leo!” Twilight called.
The Turtle Dragons taking the chance also blasted the dark ones with their magic thus destroying the medallions. The Dark Turtle Dragons started losing their magic and also fell right on top of the Technodrome destroying half of it.
Shredder freed himself of the fabric wrapping only for Krang to shrink back down and land on top of them, “No! What happened, how?” Krang asked.
“It was all full proof!” Shredder cried, before looking around, “Chrysalis, help us! Chrysalis?” he noticed a note on the ground, “Sorry, boys. But our business is concluded.”
“She betrayed us!” Krang growled.
“And now you've lost.” Leo said, as he and his bros after changing back stared them down leaving them outnumbered.
“Beaten by a bunch of ponies!” Shredder growled.
“And not just ponies.” Smolder said, as the Young Six stood triumphantly.
Shredder frowned and shouted to the students, “You stupid students! You pestering pupils! You-” he was cut off as Rockhoof whacked him on the head with his shovel. He fell to the ground with little Pinkie Pie's bouncing around his head.
“That's enough out of you, laddie!” Rockhoof scolded him
The whole group gathered together, as Leo spoke up, “Congratulations everyone. We did it!”
“Together!” Twilight added.
“Cowabunga!” the alternate turtles cheered.
Later on some of the Royal Guards were helping to clean up the debris and checking out the remains of the Technodrome.
“So what'd you do with Night Terror and the Purple Nightmares?” Keno asked the Royal Sisters.
“We sent them to a maximum security prison called Saddlecatraz Island.” Celestia answered.
“It's known for housing some of the worst Equestrian Criminals. They should feel right at home.” Luna added.
"And I assure you it's strong enough to even hold mutated ponies like them." Celestia assured.
A guard flew over, “Your excellencies.” he addressed them.
“Have you found anything?” Celestia inquired.
“Only pieces of these.” the guard showed them shattered pieces of the dark Turtles medallions.
“You think that means the Dark Turtles are gone?” April asked.
“Let's hope so.” Leo replied.
“Yeah. As much as they were challenging, I'd rather not have to deal with an evil me ever again.” Raph added.
“Or deal with them again.” Starlight motioned to the apprehended Shredder and Krang next to the alternate turtles.
“Well, guys. It's been great teaming up with you again.” Leonardo told the ponies.
“You are all welcomed here in Equestria any time.” Celestia said.
“Thanks, Princess dudette.” Michelangelo said.
“We'll be seeing you around.” Donatello said, as he opened up a portal back to their world, and they took their enemies through it before it closed.
Twilight and Leo turned to the students looking stern, which worried them. Suddenly the two smiled, as Leo spoke, “You all fought well today. You may be on your way to becoming ninjas closer than ever.”
“Agreed.” Twilight nodded.
“So then you're not going back home even after defeating Shredder and Krang?” Sandbar asked.
“Of course not,” Raph spoke up, “We still got to finish your ninja training.”
“And after all this, we need to break.” Karai added.
“Yes!” the students cheered.
“Come on, everypony! Let's go celebrate!” Pinkie cheered.
As everyone headed back to town, Mikey looked back at the demolished Technodrome feeling concerned about something. But decided not to dwell on it and followed the others.
Later on inside the cavern underneath the School of Friendship were the Dark Turtles brooding and complaining.
“Beaten by those turtles again!” Dark Raph growled.
“Not to mention, outsmarted again by my inferior double!” Dark Donnie vented his frustration.
“At least we got away.” Dark Mikey tried to look on the bright side.
“Shut up!” Dark Leo shouted, as he was trying to think.
“So what do we do now?” Dark Donnie asked their lead brother.
“Yeah. We can't live down here forever.” Dark Raph put in.
“I'm not sure. So zippit, ya mooks!” Dark Leo silenced them.
Suddenly from the shadows came a filly's voice, “Oh, no! Your two masters were defeated and your third master abandoned you. That's terrible!”
The Dark turtles drew their weapons, as Dark Leo called out, “Who's there?!”
Coming out from the shadows was a smiling Cozy Glow, “Hello. My name's Cozy Glow. Wanna be friends...” she gave a sinister grin, much to the Dark Turtles confusion.