In the Castle of Friendship in Ponyville, Princess Twilight and Spike were sitting at their thrones while accompanied by their friends whom they knew since they moved to Ponyville. However also in the room were another set of Twilight, Spike, and their friends along with another pony who was a unicorn with a light brilliant amber coat, and her mane and tail was a combination of red and yellow, with a red and yellow shimmering sun cutie mark.
The rest of the girls were wearing clothing unlike the first half. They were in fact the ponies counterparts from the human world. After the events of the Triceraton invasion which resulted in the dinosaur alien race unleashing a black hole on earth, the girls fled through the portal to Equestria for safety, but lost their home.
The CHS girls sighed still unable to bear what happened, "Come on, girls cheer up." Pinkie Pie told her transformed human self and her friends.
"How can we?" Sunset Shimmer asked.
"We lost our home, our friends, and families." CHS Rarity said, still feeling saddened by their loss.
"Yeah. Even I still can't find anything positive for this situation." CHS Pinkie Pie said feeling dismal.
"I really wish I could do something to help." Princess Twilight replied.
"Well, I'm afraid that's impossible." Sunset answered.
"And I doubt anything can help us now." CHS Twilight added.
Suddenly a light started shining in the castle, taking everyone by surprise, "What's that?" Spike asked.
"I don't know." Dog Spike answered.
That light turned into a portal that opened and what they saw on the other side were their old friends from New York city, the ninja turtles, April O'Neil and Casey Jones.
"Girls! Can you hear us?!" Leo called out.
"Leo? Guys, is that really you?" Princess Twilight asked with hope.
"Yes. Hurry and get through. There isn't much time!" Leo ordered.
"What do you think, girls?" CHS Twilight asked.
"I know we can always trust the turtles." CHS Applejack said.
"Then let's go!" Sunset Shimmer ordered.
"I'm coming too," Princess Twilight said before turning to her Ponyville friends, "You girls hold down the fort. I don't know when I'll be back. But I'll return. Come on, Spike!"
"Right!" her assistant agreed, as they headed for the portal.
"Hurry! Hurry!" Donnie cried, as the portal was getting weaker.
And so the group of pony girls and two dragons jumped into the portal before it closed, leaving the five ponies in confusion.
"So who's going to tell this to Princess Celestia?" Fluttershy asked, as they had no idea what to do.
Meanwhile the girls and Spike were flying through the portal before suddenly noticing they were changing back to their human appearances, and both Spike's became dogs.
They landed on the other side of the portal with a thud, "Will everyone get off me?!" Rarity cried.
"At least you aren't on the bottom." Twilight groaned from the bottom.
"Hang on, girls." April said, as their friends helped them up.
When they were on their feet and had balance again, they noticed their mutant friends, "Guys! It's you!" Pinkie cried.
"Pinkie!" Mikey cried, as the two embraced and laughed.
The rest of the girls embraced the turtles, April, and Casey, "It's so good to see you all." Rarity said with joy.
"And it's great to see you too." April agreed.
Raph looked ahead and saw another Twilight wearing glasses and had her hair in a ponytail, "Twilight?" he looked seeing the Twilight they already knew, "Twilight?"
"Twilight?" the mutants asked in confusion.
"Pinkie!" Pinkie jumped up and cheered.
The girls rolled their eyes, as Leo spoke, "Two Twilight's? What's going on here?"
"A clone?" Casey asked.
"Not exactly," Princess Twilight began, as she showed her human counterpart over, "This is actually my counterpart from this world."
"Whoa. Freaky." Mikey gasped, only to get slapped in the head by Raph.
"Um, are these really?" Twilight began.
"Yeah, these here are the friends we told ya about." Applejack began.
Rainbow introduced them, "That's Leonardo, Raphael, Donatello, Michelangelo, April, and Casey."
"Amazing, actual mutant terrapins." Twilight gasped, as she straightened her glasses.
Casey noticed the two dogs, "Hey, Spike. So is this also?"
"Yeah, this guy here's my counterpart from this world." Spike introduced him.
"Hi there." Dog Spike barked.
Casey jumped back, "Whoa! He can talk too?"
"Yeah. But I couldn't always talk like this." Dog Spike answered.
"Um where are we?" Fluttershy wondered.
They looked around seeing they were on a space ship, "It looks like a space craft." Twilight said in amaze.
"Space craft?" the girls asked together.
"But that would mean..." Applejack began only to get cut off by Pinkie Pie.
"Girls, look at this!"
They turned and saw Pinkie gazing out the window of the ship with her face pressed against the glass. They ran over to the window and looked out seeing the vast depths of outer space.
"No way!" Rainbow gasped.
"We're in outer space?!" Twilight gasped in amaze.
"This is unbelievable!" Sunset gasped.
"But it's real." Donnie assured.
"Ok, guys. What're you doing up here in space?" Rainbow asked, "Or how did you get up here, and how did you bring us here?"
"How we got here is quite the story," Donnie began, "But we managed to get you here through a Time Dimensional Portal that penetrated the barrier between our world and Equestria through time and space."
"But how were you able to pull it off?" Princess Twilight asked.
"That would be me, my dear." came a new voice.
Everyone looked ahead and saw coming down some stairs and into the bridge was a six foot tall robot that was slender-built. He had a rounded head and armored arms and legs. His body parts were colored opalescent white. His eyes were glassy light board dark with orange lights. His eyes and mouth looked light bulb pixels.
The Rainbooms were surprised at the sight of the robot, as it spoke again, "Greetings, girls. My name is Professor Zayton Honeycutt. But you can call me Fugitoid. Welcome aboard my ship, The Ulixes."
"Wowee zowee! A robot?!" Pinkie gasped.
"Amazing!" Twilight ran to the Fugitoid and examined him, "An actual fully sentient multi-functional automaton!"
"I'd still prefer Fugitoid, thank you, Ms. Sparkle."
"You know me?" she gasped.
"Of course. I know all of you thanks to my friends here." Fugitoid motioned to the Turtles.
"Would you all please explain what's going on?" Rarity asked politely.
"Well, you all had to know what happened to earth." Leo answered.
"We do." Applejack sighed.
"But how did this happen at all?" Twilight asked.
"Sit down, girls. There's a lot to talk about." Leo instructed.
So the group sat down, as Leo and his brothers told the girls precisely what went on during the Triceraton invasion from their POV. Needless to say the girls were shocked and surprised to have heard what led to the destruction of the planet.
"So that's it?" Princess Twilight gasped.
"That about sums it up." Donnie answered with a sigh.
Rainbow Dash frowned and kicked one of the stations seats with a grunt, "I can't believe this! I can't believe Shredder doomed the planet!"
"That yellow bellied snake in the grass!" Applejack expressed her anger towards the mad man.
"He allowed the destruction of the planet over any chance of seeing Karai again?" Fluttershy asked in disbelief.
"I guess his thirst for revenge was too strong." Princess Twilight sighed.
"Don't worry, when we stop all this and get back to earth we'll make sure Shredder pays." Raph promised.
"I just can't believe it. Splinter is actually gone." Sunset Shimmer said with sorrow.
"Was gone," Leo corrected her, "But thanks to Fugitoid we have six months to stop the Triceratons from destroying the earth."
"We just have to find the black hole generator pieces." April added.
"And by destroying them, the earth will be unharmed." Fugitoid finished.
"Well, you can count on us to help you." Princess Twilight promised.
"Thanks, girls. We knew we could count on you." Leo smiled.
"That's us for you. Loyal to the end." Rainbow declared, before she started glowing.
"Rainbow Dash?" Mikey asked.
"Don't worry, this is normal for us." Rainbow answered, as she floated up and gained her pony features before landing.
"Fascinating." Fugitoid gasped.
"You ponied up!" Casey said with excitement.
"But how?" Raph asked.
"Yeah. Don't you only do that when you play music?" Mikey asked.
"We first thought that was the only way," Sunset explained, "But we found out we can pony up by just expressing who we really are."
"Based off the element of harmony you represent." Donnie realized.
"Exactly." Princess Twilight confirmed.
"So how exactly did ya manage to find us?" Applejack asked.
Fugitoid elaborated, "While scanning around through the vast dimensions in search for the the black hole pieces we happened across an odd anomaly coming from a particular dimension that was all the way in the future."
"We learned it was you girls coming from Equestria in the future we're trying to prevent." Donnie put in.
"We're just glad you were all ok." Raph said.
"Yeah. What happened to you all?" April inquired.
The girls sighed, "I guess you could say what happened with us is exactly what happened ot the rest of your friends." Sunset explained.
The girls flashed back to what was going on at CHS when the Black Hole generator was set off and started sucking everything into the sky.
The faculty and students were trying to take cover, as Lyra cried in a panic, "We're done for!"
Bonbon embraced Lyra, "Hold me close, Lyra!" the girls screamed, as they were pulled up into the sky.
Sandalwood and Micro Chips who were hanging onto a tree branch each lost their grip and were getting sucked up too. Lyra and Bonbon were the first two to get swallowed up into the black hole followed by Sandalwood and Micro Chips.
One by one the various students and teachers were getting swallowed up, as the Rainbooms took cover, "What do we do now?!" Fluttershy cried.
"Applejack!"
"Rarity!"
"Rainbow Dash!"
The three girls looked over, and saw Applebloom, Sweetie Belle, and Scootaloo holding onto a bench for their lives.
"Girls, hang on!" Rainbow called.
"We can't!" Scootaloo cried, until the three lost their grip and got swallowed up into the black hole screaming.
"NO!" Applejack and Rarity cried with tears in their eyes.
"Girls!" they heard a voice. They saw it was from Principal Celestia who was holding onto a tree with Vice Principal Luna, "You have to get out of here! Go through the portal to Princess Twilight's home!" the principal ordered.
"What about all of you?" Sunset Shimmer called.
"There's no helping us now. You have to go and save yourselves. Maybe Twilight can find a way to stop this." VP Luna called.
"We can't just leave you all!" Rainbow replied.
"That's an order as your principal!" Celestia ordered, "Now hurry!" she and Luna lost grip and got swallowed up into the black hole.
"Girls, we have to go!" Sunset called, as she eyed the portal to Equestria.
"Looks like there's no choice." Applejack said, feeling sad for not being able to help her sister or the rest of her family.
So they ran for the portal despite the strong vacuuming force that was trying to pull them in. They all just managed to jump through the portal before the statue was pulled off from the pavement and into the black hole with everything else.
It cut back to their time, as the turtles were distraught, "Oh, man." Mikey gasped.
"We're so sorry, girls." Leo apologized.
"Watching everyone get sucked up like that, it was just so..." Fluttershy trailed off while looking ready to burst into tears.
"We know how ya feel." Raph comforted her.
"But it can all be avoided." Leo brightened their spirits.
Princess Twilight stood up, "Leo's right. If we can destroy the heart of darkness before the Triceratons find the pieces then planet earth is safe."
"Well count me in on saving the earth." Rainbow stepped forward.
"Me two." Applejack stood by Rainbow Dash.
"Me two too." Pinkie said.
"I'll do it for all the animals of planet earth." Fluttershy added.
"And for everyone as well." Rarity put in.
"We'll all do it." Sunset offered.
"I'm not sure how much help I can offer compared to me friends," Twilight said feeling unsure before looking determined, "But I'll do whatever I can."
"And we'll help too." Spike said.
"We sure will." Dog Spike agreed.
"Oh yeah!" Mikey cheered, "The whole gang's back together again!"
"With all of us together those Triceratons won't know what hit 'em!" Casey cheered.
"Hands in everyone." Mikey called, as the whole group put their hands in, before Mikey turned to their robot friend, "Come on Fugitoid, you too."
"Oh, thank you." Fugitoid's eyes lit up making it look like he was smiling, before laying his hand on top.
"Booyakasha!" they announced together.