One day in Ponyville, the ninjas were wandering about greeting any of their pony friends that passed by, “Another peaceful day in Ponyville, eh, bros?” Mikey asked joyfully.
“Yeah, boring.” Raph grumbled.
“Hey, it gives us a chance to relax.” Donnie reminded him.
“Especially with all that's been going on.” Leo reminded him.
“Well, I'm all for relaxing, but even if it looks alright we still have two enemies out there after us.” Raph reminded back.
“Stressing about it won't help at all, Raph.” Sunset noted.
“Quite right. So let's enjoy this day without any possibility of problems springing up.” Fugitoid said, until a voice gasped.
“Oh my gosh it really is you!” the ninjas stopped in place before seeing a photographer pony galloping over, “The famous Equestrian Ninjas, right?” she asked all excited.
“Yeah. That's us,” Leo confirmed, while sounding disturbed by her excitement, “And you are?”
“Oh, forgive me, where are my manners?” she asked, “I am a photographer for the Equestrian Daily, and I was wondering if you four ninjas would like to be in an article for the next issue?”
“What's the article about?” Donnie inquired.
“Equestrian heroes of course. I once did an photography shoot for Princess Twilight Sparkle and her friends, but now we have more celebrity heroes.”
The four brothers looked at each other oddly, as Leo spoke, “Well, if it's for good press, ok.”
“Yes!” the photographer said, as she took quick shots of each other the turtle ponies while secretly snipping a bit of hair from their heads, “Thank you so much for your time.” she took off.
“She was in such a hurry.” Karai noted.
“Doesn't anybody think something's off about this?” April asked.
“Yeah, like why weren't we asked to be in the article?” Casey asked sounding jealous.
“Da, is we not good enough?” Rocksteady asked.
“I sure feel insulted.” Bebop crossed his arms.
“Guess that photographer pony heard of my mad skills.” Mikey boasted.
“Don't flatter yourself.” Raph replied, as they walked on.
Meanwhile, the photographer pony ran from from Ponyville and to the Everfree Forest where Krang and Shredder were waiting, “Well, did you get what you needed?” Shredder inquired.
The photographer pony changed shape and was Chrysalis who was smirking, “Oh, yes. I have all that I need to put the plan into motion.”
“Excellent.” Krang snickered.
“Now onto phase two.” Chrysalis said, as she led the two away.
Soon they were walking through Everfree while stopping before a bunch of trees. Shredder spoke to the former Queen, “Are you absolutely sure this plan of yours will work?”
Chrysalis looked back and explained, “First time I tried this I wanted to harness the power of the Elements of Harmony which came from the Tree of Harmony. However only Twilight and her five friends were capable of harnessing them and knew where the tree was. So I gathered the materials in order to create clones of them so they would be able to use the elements for me.”
“And how did that work out?” Krang asked.
Chrysalis sighed, “Sadly not the way I hoped. While the experiment worked I ended up creating bad clones of the girls. But not only were they bad, they were the complete opposite of Twilight and her friends.”
“Opposite how?” Shredder wondered.
Chrysalis frowned to herself and explained, “The clone of Applejack was nothing but a liar, Rainbow Dash's clone was lazy and ditched us, Pinkie Pie's was a big grump, Fluttershy's was mean which I'm glad she was, Rarity's was greedy, but Twilight's clone was deceptive and double-crossing. I sent them to try and get information from the real ones on the whereabouts of the tree, but due to their opposite nature made it difficult for them to complete their task and raise suspicion from the real ones.”
“And they didn't see right through the fakes?” Krang wondered.
“No, which to this day surprises me. They just assumed each other was acting up because of frustration. Then when I finally got the location of the Tree of Harmony, I took the clones there and ordered them to harness their powers for me. But they turned on me and wanted to use the elements themselves. Thankfully they never got the chance too.”
“And why not?” Shredder asked.
“The Tree of Harmony is more sentient than any of us thought, and could tell right away my clones of the girls were evil and fakes. And it ended up turning the clones into colored pieces of wood. I knew there was no chance I'd be able to harness the elements so I left and never looked back.”
“In other words your plan backfired.” Shredder noted.
Chrysalis frowned at him, before speaking, “I had since then perfected the spell I used to create them and now am ready to create new clones. Clones of those blasted ninjas who defeated us. Only this time not only will they be evil, but more loyal than my last gang of clones.”
“We'll believe it when we see it.” Krang said.
“And you shall,” Chrysalis said, as she pinned each picture of the turtles to a tree each along with their hair lock onto the picture of the turtle they belonged to, “One final touch.” she used her magic to carve an image of each of the turtles cutie marks onto the trees. She stood in between the four trees and released her magic onto them. The trees connected to form a circle before green glowing cracks appeared on them.
Shredder and Krang watched in shock, as the trees cracked open, and climbing out were four figures who growled and groaned. Chrysalis looked around and smirked, “Yes. Welcome my new servants. My partners and I have a job for you.” she snickered.
The very next day, the girls, Spike, and the New York team were on the train bound for the Crystal Empire, “I can't wait till we get to the Crystal Empire.” Mikey said all giddy.
“Me too!” Pinkie beamed.
“And this Empire is ruled by Twilight's brother and sister-in-law?” Keno asked.
“Correct.” Leo confirmed.
“Plus we need to keep them briefed about Shredder and Krang as well.” Twilight added.
“Plus, we gets to see another kingdom in Equestria.” Rocksteady said on behalf of himself and Bebop.
“Yeah. Another place to show off our sweet heroic skills.” Bebop added.
The train pulled into the station and the whole group got off and walked through the kingdom. As they walked Keno, Fugitoid, Bebop, and Rocksteady were taking in their surroundings.
“This empire is so lovely.” Fugitoid marveled.
“Yeah, and sparkly.” Rocksteady agreed.
“Makes me wish I was wearing shades.” Keno said.
Bebop took notice of Spike's statue, “Dang, Spike-O, you got yourself a statue here?”
“Yeah. I'm kinda a celebrity here.” Spike admitted.
“Your statue didn't have that the last time we were here.” Leo took notice that the statue of Spike now had wings.
“You're right. It didn't,” Spike realized, before turning to Twilight, “Twilight?”
“After you got your wings I did tell the Princesses, and Cadence made sure that the statue of you was up to date with your current look.”
“Well, I like it.” Spike replied, while smiling at his statue.
“Spike the Brave and Glorious!” voices cheered, as Crystal Ponies started swarming around Spike greeting him and posing for pictures with him.
“It's just as the Princess said, you have wings now.” a mare marveled at his wings.
“They look perfect.” another pony admired them.
Twilight broke the crowd up and got Spike away form them, “Alright, everypony let's calm down. We have other business to attend to.” and with that they headed for the castle.
Once they entered the castle, they walked through the hall before opening the doors to the throne room where the royal couple, Blade, Sunburst, and Flurry Heart in her crib was waiting.
The couple approached the group and hugged Twilight, “Twily, good to see you,” Shining Armor greeted her, “And everypony else.”
“Leo, we haven't seen you and the others since the Festival of Friendship.” Cadence greeted him.
“I know. How time flies.” Leo joked.
Sunburst took notice of the newcomers, “I definitely don't remember seeing some of you.”
“That's because they're new additions to the ninja team who weren't able to come here last time.” Sunset Shimmer explained.
Fugitoid approached, “Princess Cadence, good to see you again.”
“Same to you, Professor Honeycutt.” Cadence greeted.
Shining Armor approached, “So you're the Fugitoid, huh? I've heard a lot about you from Twilight.”
“Well, I'm not surprised to know that.” Fugitoid noted.
Keno approached, “My name's Keno, top vigilante in New York.”
“Yeah right!” Casey shoved him, “You're only second rate, bro!” the two glared at each other, until April and Sunset came between them.
“All right, you two, that's enough.” April calmed them.
Sunset turned to the couple, “You have to excuse these two. They have a rivalry.”
Sunburst noticed Bebop and Rocksteady, “Oh my gosh. You brought two more mutant ponies?”
“Sort of.” Donnie answered.
Rocksteady spoke up, “We is the Bebop and Rocksteady; former henchmen of Shredder before becoming the good guys.”
“Nice to meetcha.” Bebop greeted.
Cadence smiled and approached, “It's very nice to meet you too. I'm Princess Cadence, and this is my husband Shining Armor, our Crystaller Sunburst...” before she could finish, Bebop noticed the crib.
“Hey. What's in there?” he asked.
Cadence looked over and smiled, “Would you like to see?” the two mutants, cyborg, and vigilante nodded, as they were led over to the crib and saw the little foal in it, “Meet our daughter, Flurryheart.” the baby giggled, as it looked up at the four newcomers.
“How remarkable.” Fugitoid gasped.
“Wow.” Keno gasped.
“Oh, comrade, look at the cute baby pony.” Rocksteady cooed at Flurry.
“Her wings look a little big for her.” Bebop noticed.
“Yeah, but she knows how to use them.” Rainbow warned them.
Keno spoke to the couple, “So the two of you rule this kingdom together?”
“Yeah ever since it resurfaced after a thousand years.” Shining Armor explained.
“All because of King Sombra.” Fugitoid recalled the history Princess Twilight informed him of.
“Ruling Kingdom and being parents must be tough job.” Rocksteady said.
“It can be stressful, but it's all worth it in the end.” Cadence said, as she picked her daughter up.
Flurry giggled, as she poofed out of her mom's hold and appeared atop Rocksteady's head, “Hey, what is this?” Rocksteady asked, as he picked the foal off his head and held her. The baby giggled, as Rocksteady smiled, “Aren't you the cute?” he cooed at her.
Flurry poofed away again and reappeared in Bebop's arms, “Dang, she's quick.” the former master thief gasped.
“You have no idea.” Twilight replied, recalling the day of her Crystalling.
Blade Swipe spoke to the group, “Princess Celestia and Princess Luna sent me ahead to inform them of the dangers you told us about.”
“This Shredder and Krang sound like trouble from what he told us straight from your mouth.” Shining Armor told Twilight.
“And they are.” Leo confirmed.
“We're not sure where they are right now, but we can be sure they're planning something.” Donnie said suspiciously.
“Well, you can be sure we'll help out in any way we can.” Cadence promised, as the group smiled.
“Thanks, you guys.” Leo said gratefully.
“So we gonna get some tour of this kingdom or what?” Bebop asked.
The couple smiled, as Cadence answered, “Of course. Sunburst, Blade, would you please help show our new guests around?”
“Sure thing, Princess.” Sunburst agreed.
“I'd be delighted.” Blade added, as the group trotted off.
Later out in the kingdom, Sunburst was helping the others show Bebop, Rocksteady, Keno, and Fugitoid around, “This kingdom is so fascinating. Almost as great as Canterlot.” Fugitoid marveled.
“We've only been there once, but we can agree.” Bebop said on behalf of himself and Rocksteady.
As Spike followed behind the group, he heard a voice call out, “Hey, are you Spike the Brave and Glorious?”
Spike looked back and saw a silhouette of someone around a corner, “Uh, yes.” he answered.
“Awesome! Can I have a picture with you?” the figure asked hopefully.
Spike smiled, “Well, I never pass a chance to do something for a fan,” he hurried to the corner and went around it, “So about that pic-ture!” he screamed, as a huge silhouette fell over him.
Back with the group, Karai looked around and saw they were one member short, “Anybody seen Spike?”
“Spike?” Twilight asked, as they saw no sign of him.
“Where'd he go?” Rainbow asked.
“Don't tell me we lost him?” Raph groaned.
“He can't have gone far.” Shini said.
“Come on, let's find him.” Leo ordered, as they searched around.
“Spike!” Twilight and the girls called.
“Where are ya, Spike?” Mikey called out.
“You around here?” Casey called out.
“Comrade Spike!” Rocksteady called, while looking in a bush.
“Dragon dude, where are ya?” Bebop looked around.
Fugitoid looked around before stepping on something. He looked down and saw a slip of paper. He picked it up and looked at it and gasped, “Everyone, over here!”
The group ran to Fugitoid's location, as Sunset asked, “What's up, Professor?”
“You find Spike?” April asked.
“No, but I found this.” Fugitoid showed them the note.
“A note?” Applejack asked, as Twilight read it.
“We have your dragon friend. If you want him back come down to the Crystal Catacombs under the kingdom. And don't think about going to the royal couple, or your dragon friend's gonna be scaleless for life.”
The group gasped at the threat, until Rarity frowned and shouted, “If these perpetrators harms one scale on my Spikey Wikey, I'll rip them to pieces!”
“Took the words out of my mouth.” Raph agreed.
“What're the Crystal Catacombs?” Keno asked Twilight.
“The underground caverns underneath the empire.” Twilight explained.
“We should warn Cadence and Shining Armor.” Sunburst suggested.
“You heard what the note said,” Starlight reminded him, “We go to them and they'll hurt Spike.”
“We can't risk it.” Blade agreed.
“Come on, we have to hurry.” Twilight ordered, as she led the way.
The group found the entrance to the catacombs, and proceeded with Twilight, Rarity, Sunburst, Starlight, Sunset Shimmer, Blade, April, and Rocksteady were using their horns to project light, while Fugitoid was using his eyes to project light as well.
As they walked through the dark crystal catacombs, the ninjas were looking spooked, with Mikey trying hard not to panic, “Jeez, a place like this is under the Crystal Empire?” Casey asked.
“It is said King Sombra had buried the remains of deceased crystal ponies who worked themselves till they expired.” Sunburst noted.
“Oh, that's great.” Raph answered sarcastically.
“You could get lost down here.” Bebop said, as he kept his eyes peeled.
“Exactly, so stay together.” Twilight ordered, as they pressed on.
“Does anyone have that feeling we're walking into a trap?” Sunset asked rhetorically.
“Don't we always?” Karai answered.
“Good point.”
They continued on before entering a chamber. April suddenly clenched her forehead with her hoof, "April?" Donnie asked, in concern.
"We've got company." she replied.
"Where?" Twilight asked, as the group was cautious.
Before April could answer, something rushed past them from behind them, "What in tarnation?" Applejack asked in surprise.
Another thing ran past them. This time from the front. Another one flipped over a ledge, above them. Then finally, another swung from a higher platform onto another. Laughter echoed, all around them as Fluttershy started to cower underneath Rainbow Dash.
"Who's there?!" Raph called out.
"If your trying to scare us, then I'm afraid you'll be very disappointed," Keno boasted, "Cause the Night Watcher isn't so easily scared!"
"Is that so?" came a voice, that sounded just like Mikey's.
Everyone turned to an entrance to another tunnel. Keno walked closer for a better look. Then suddenly... "Boga-boga-boga!" Keno screamed and jumped away behind Starlight who rolled her eyes.
What jumped out at him, stretching out it's mouth, left everyone in shock. It was another Mikey!
Or was it?
It sure looked like Mikey. But instead of being green, he was dark yellow, with a pair of double bladed battle clubs strapped to his back. He had sharp teeth with a two foot tongue hanging out of his mouth.
The other Mikey laughed, "So much for the fearless Night Watcher!" he mocked.
Before anyone could say anything, a figure dropped down onto a ruined pillar. It was another Leo! And landing next to him was another Donnie! Then smashing through a crystal wall was another Raph!
Like the other Mikey, they also looked different.
The other Raph was dark red, with small horns on his head and cheeks, and big sharp thumbnails. And on his belt were two large Honshu Tanto Blades. He also looked much angrier than Raph.
The other Donnie was dark purple, with sharp metal bracelets, and a long lizard tail. And like Donnie, he also had a gap in his sharp teeth. He also carried a Jagged Spear.
And the other Leo was dark blue, with a pointed metal shoulder pad, and had two Twin-Bladed Swords strapped to his back.
All four had black manes and wore black masks.
The other Mikey did flips, twirls, and midair somersaults all around the group, while laughing like a maniac. Still laughing, he flipped by the other Turtles and began banging his clubs around, "Sea Beagle!" he shouted, randomly.
"Wow. For once I did not see that coming." Pinkie said in shock.
"Who are you?" Leo asked, in surprise.
"I guess you can call us your brothers." the other Leo said, smugly.
"Only smarter, stronger, and more efficient!" the other Donnie, rudely stated.
"Cloned from your tissues, with lots of issues!" the other Mikey gave off another crazy laugh.
"Wait a minute, clones?" Donnie asked, in confusion.
"Not clones, D," Mikey said, in worry, "They are, The Dark Turtles!" the group looked at him oddly.
"Dark Turtles? Lame!" the other Mikey said, in disgust.
"The Dark Turtles?" the other Leo echoed. "Sounds good, we'll take it!"
"ENOUGH YAKING!" the other Raph shouted, "WHICH ONE OF YOU IS RAPHAEL?"
"That would be me." Raph pulled out his sais, ready to fight.
Twilight raised her wing to block Raph's path, "We don't have time for this, Raph. We need to find Spike."
"So you lost your little dragon, did you?" Dark Leo asked.
"What? How do you know..." Twilight got the hint. She gritted her teeth and charged up her horn, "You're the one's who took him!"
"Guilty," Dark Donnie replied, in singsong, "Oh, but don't worry, he's alright... for now!"
"Where is he?!" Twilight demanded.
"Let us answer that by making you guys an offer." Dark Leo began.
"One we can do the easy way." said Dark Donnie.
"OR THE HARD WAY!" growled Dark Raph.
"Or the crazy way!" laughed Dark Mikey, until Dark Raph punched him aside.
"We'll give you Spike, for the Turtles and Starlight." Dark Leo said, while motioning to said friends.
"What?!" Starlight cried.
"Absolutely not!" Twilight refused, "You're not getting Starlight."
"Or us!" Leo agreed.
Dark Leo grinned, "We were hoping you'd choose the hard way." And the Dark Turtles drew their weapons.
"If it's a fight you want, we'll bring it to yah!" Raph said ready to fight..
"Yeah, we got you totally out numbered." Rainbow Dash noted how they had the four outmatched.
"Oh, that reminds me," Dark Donnie pulled out some strange black rocks, "No interlopers!" He threw the rocks into the ground close to Twilight and the others. Before anyone could understand what was happening, large black crystals sprouted up all around the ponies, trapping them inside.
"Girls!" the Turtles cried.
"What's going on here?" asked Keno.
Starlight tried to teleport out, only to suddenly teleport right back in, "What? That should have worked!" she said, in disbelief.
"Oh, no! These must be Sombra Crystals," Twilight realized "Teleportation spells are useless on them!"
"That's right," called Dark Donnie "And in case any of you birdie ponies think about flying out, the top is sealed up! So you can't. Oh, and one more thing." Dark Donnie rolled out a huge rock. Then suddenly, the Turtles weapons, and even medallions were pulled from their hands or around their necks and stuck to the rock.
"What the?" Raph asked in confusion.
"My chucks!" cried Mikey.
"What just happened?" asked Leo.
"That rock must have some kind of magnetic properties," Donnie theorized. "Anyone else think we just got set up?"
"Right again," Dark Donnie chucked meanly, "Did you honestly think we would make this easy for you?"
"And now that we have you at a disadvantage." Dark Leo began.
"LET'S CRUSH THEM!" Dark Raph finished.
"Dibs on my doppelganger!" added Dark Mikey.
"Without our weapons and medallions, we're basically defenseless!" Donnie panicked.
"We've got something they don't have," Leo said "A real reason to fight. For Spike! Ninjas, take 'em down!"
The two turtle teams charged at each other. While Twilight and the others could do nothing but watch through the crystals and hope their friends would be okay.