One day, the Rainbooms, the Shadowbolts, Fugitoid, Starlight, and Juniper were on their way to the lair. This time, however, they were accompanied by another group composed of Flash Sentry, Sandalwood, Micro Chips, Derpy, Lyra, Bonbon, Applebloom, Sweetie Belle, and Scootaloo. Flash spoke to the girls, "Thanks for not ditching us to sneak off by yourselves."
"Well, since you guys already know the turtles there's no point in hiding it from you." Sunset answered.
"Well, we don't know anything about these turtles other than what ya told us." Applebloom said.
"Trust me, Applebloom, you're gonna love them." Applejack said.
"With all you told us about them, we can believe it." Scootaloo replied, as they happened upon the sewer.
"This is the spot?" Lyra asked.
"Closest to get us to the lair." Rainbow answered.
Applejack lifted up the cover, and they started climbing down. When the ninjas were in the sewer, Fugitoid spoke to the third group, "Step lively now." Flash and the others went down into the sewer slowly.
When they all reached the bottom, Sweetie Belle looked around, "Yuck. And you actually come down here, Rarity?"
"Yes, I know, but it's not so bad once you get used to it." she replied.
"Well, girls, lead the way." Bonbon said, as the group led their classmates through the sewer system.
Meanwhile in the turtles lair, the bros were relaxing while enjoying some cartoons, until they heard Twilight's voice, "Hey, guys!"
The brothers saw their friends enter, "Hey, girls, how's it going?" Leo asked.
"All good. Whatcha up to?" Pinkie wondered.
"Just chillaxing." Mikey answered.
"I hope you don't mind, but we brought some old friends." Sunset began, as the third group walked in.
"What? You brought them?" Raph asked in shock.
"Come on, Raph, they know who you guys are and vice versa." Rainbow replied.
"Hey, guys, it's good to see you again." Flash said, as he and Leo shook hands.
"Nice to see you again, Flash. And the rest of you." he spoke to the others.
"So this is where you guys live?" Micro Chips asked, while looking around.
"Yup. Born and raised here." Mikey boasted.
"Not really born here, but we were raised here." Donnie replied.
"Not bad for a sewer lair." Sandalwood admitted.
"This place is cool." Scootaloo said, while looking around.
The turtles noticed the three younger girls, "Aren't they?" Leo wondered.
"That's right," Applejack replied, "This here's my little sister Applebloom."
Rarity brought Sweetie Belle over, "This is Sweetie Belle, my darling little sister."
Rainbow spoke while putting an arm around Scootaloo, "And this is Scootaloo, my number one fan."
Applejack spoke to the three, "Girls, these are the turtles. Leonardo, Donatello, Michelangelo, and Raphael."
Leo spoke to the three, "It's nice to meet you three. Your sisters have told us much about you."
"They did?" Sweetie Belle asked.
"Yeah. You girls like to get involved into a lot of things." Donnie said.
"Yeah. We do a lot of stuff back home," Applebloom admitted, "But what we're really known for is the CMC!"
"CMC?" Raph asked.
The trio announced, "The Canterlot Movie Club!"
Mikey whispered to his bros, "Guess they can't call themselves Cutie Mark Crusaders in this world, can they?"
"So what brings the rest of you here?" Leo asked the other students.
Bonbon answered, "Well our group was paired to be with their groups, and they didn't wanna leave us hanging just to sneak off to see you guys."
Lyra continued, "Since we already know each other it wouldn't be bad that we joined them."
"Well, good point." Donnie admitted.
"We heard what's been going on with you guys as of late." Micro Chips said.
Sandalwood spoke, "Sorry to hear about Master Splinter."
"Thanks. It hasn't been easy, but we've managed to continue on." Leo admitted.
"So, you girls wanna get some training in?" Raph asked.
"You know it." Sour answered.
"Think we can train too?" Flash asked.
"Yeah. I wanna put some more meat on my bones." Micro Chips added.
"What do you say, Leo?" Twilight asked him.
"Well, more the merrier." Leo answered.
"Yes!" Lyra and Bonbon cheered.
Soon enough the girls along with their fellow classmates were getting some ninja training in. Flash and the others were doing hand to hand moves with Leo, Twilight, Rainbow, and Raph teaching them. Micro Chips spoke to the others, "This ain't so bad."
"This is only beginners stuff." Raph replied.
"Trust me, the advanced stuff is no picnic." Twilight assured them.
"Hey, guys!" Applebloom called, as she and her friends entered the dojo with Mikey, "Check out the cool weapons Mikey gave us." She held up a single tanto sword, while Scootaloo had two butterfly knives like Xever had, while Sweetie Belle had Nekode Finger Nail Claws on all ten of her fingers.
The group was shocked at this, as the turtles shouted, "Mikey!"
"What? Just let the kids have some fun," Mikey answered, "Besides it's not like they're gonna hurt themselves."
"I wish you'd consult with us before giving our sisters ninja weapons." Rarity scolded him.
"Actually, I don't mind it." Rainbow admitted.
"Rainbow!" Applejack chided her.
"What? We all have weapons, and we're good with them." Rainbow reminded them.
The girls sighed at her lack of safety, until they heard a familiar voice from the living room, "Hello? Anybody home?"
Recognizing the voice the group left the dojo and saw Slash and the Mutanimals entering the lair, "Greetings, turtles." Slash greeted his fellow mutants.
Sandalwood spoke to his fellow students, "Dudes, it's the Mighty Mutanimals."
Slash noticed their human friends, "Didn't know you guys were entertaining. Rainbooms, good to see ya again."
"Same to you guys." Sunset answered.
Fluttershy went over and hugged Slash's arm, "I missed you, Slash."
"I missed you too, Fluttershy." Slash replied happily.
"Leatherhead!" Pinkie cheered, as she ran over and hugged the big gator.
"Good to see you, Pinkie Pie." Leatherhead greeted her.
Rainbow walked up to Rockwell, "Hey, what's up, doc?" she joked, while raising a fist.
"Oh, how original, Dash." Rockwell replied sarcastically, as they fist bumped.
Pigeon Pete was suddenly embraced by Derpy, "Aw!" he said happily as he hugged her back.
Mondo spotted the two girl besties, "Now there's a pair of girls I recognize!" he ran over and jumped into an embrace with Lyra and Bonbon.
"It's great to see you, Mondo." Bonbon said, as she and Lyra embraced him.
The Rainbooms and Fugitoid spotted their Salamandrian ally and Raph's love interest, "Mona Lisa!" the girls gathered around her.
"My old friends, the Rainbooms," she began, "It's been a long time."
"It's great to see ya." Applejack said.
"We heard you were kicking it here in New York for awhile." Rainbow noted.
"Yes. By Raphael's suggestion and my own choice, I decided to remain here on earth as part of the Mighty Mutanimals."
"You suggested, huh?" Pinkie nudged Raph.
"Yeah, so?" he asked.
"Nothing." she grinned.
Sour spoke to Leo, "There are even more mutants in the city?"
"Yeah, but these guys are our allies. They're called the Mighty Mutanimals," Leo began introducing, "This is Slash, Leatherhead, Dr. Rockwell, Pigeon Pete, Mondo Gecko, and Mona Lisa."
Twilight spoke to the mutant team, "And you already know our fellow classmates from camp. The rest of them here are other friends and allies. Here's Sour Sweet, Sunny Flare, Sugarcoat, Indigo Zap, Lemon Zest, Starlight Glimmer, Juniper Montage, Applebloom, Sweetie Belle, and Scootaloo."
"Nice to meet you all," Slash greeted, before turning to Starlight, "You're Princess Twilight's pupil, right?"
"Yeah, that's me." Starlight confirmed.
"How is she doing these days?"
"Oh, same old." she answered.
Fugitoid approached, "Ah, the famous Mighty Mutanimals, I'm delighted to finally meet you."
"Aren't you the Fugitoid who took the past versions of our friends out into space?" Rockwell asked.
"Actually, Rockwell, this is the Fugitoid who sacrificed himself to save our planet." Donnie corrected.
Mona Lisa spoke, "But how are you still alive?"
"Fortunately my head and brain remained intact and after several months of floating above the planet's atmosphere I finally fell to earth. Sunset Shimmer found me and thanks to her and Twilight here they constructed a new body for me."
"Well, it's good to see you again, Professor." she said.
Soon enough the groups were once again bonding, as Micro Chips spoke to Mona, "So you're an actual alien?"
"Correct. I am a Salamandrian from the planet Salamandria. We are a race of honorable soldiers who want what's best for our people. Unlike those loathsome Triceratons who cared nothing for the safety of others as long as they get what they want."
"It's amazing, how many alien species actually exist in the universe." Juniper marveled.
"So how did you get attracted to Raph?" Derpy wondered.
Mona smiled, as she glanced over at Raph who was chasing Mikey around the lair, "I fell for his bravery and determination."
Mondo was currently doing some skateboard tricks for the Shadowbolts with Indigo and Lemon applauding him, "Thank you, ladies." he declared.
"You could go pro with moves like that." Lemon said.
"Thanks. And I totally could." Mondo boasted.
Sunset looked at her watch and noticed the time, "Oh, my gosh, it's getting late. We better get back to the hotel, guys."
The group groaned, until Leo spoke, "She's right. We don't want your principals to get suspicious."
"I'm sure if Principal Celestia and Vice Principal Luna knew where we were they would let it slide." Rainbow noted.
"Yeah, but what about Principal Cadence?" Sugarcoat asked.
"She's right. She doesn't know about you guys. So let's not draw suspicion." Twilight agreed.
"Well, it was nice seeing you all." Slash said, as Fluttershy joined the others.
"Hope we see you again." Applebloom said, as the humans left the lair.
As the group climbed out of the sewer, they started heading back for the hotel, "Nice to see the kind of allies we have in this city." Flash said.
"And who make it safer." Twilight added.
"They were so awesome." Scootaloo smiled.
"I know, right?" Rainbow asked while ruffling her hair.
They continued on until they heard a sound, "What's that?" Lyra asked.
"It's coming from over there." Bonbon motioned to a dumpster.
"Do we dare find out what it is?" Rarity asked in worry.
"Probably a homeless person." Rainbow said.
Suddenly the dumpster lid opened, and jumping out from it was a giant purple ant mutant. The sight of it made several of the girls scream, before calming down, "What is that?" Sandalwood asked in shock.
"A bug mutant." Sunset said, as she and the girls armed themselves.
"Think you should call the turtles?" Micro Chips asked.
"Micro Chips, it's just one mutant." Rainbow answered.
"And he doesn't look so tough." Sour added.
The ant mutant took them by surprise, as it's backside opened a bit and crawling out from it were duplicates of itself. The sight made Rarity green in the face, "That is the most disgusting sight I've ever seen!"
"Seriously, that's just gross." Sunny Flare agreed feeling equally disgusted.
Soon where one ant mutant was stood over a dozen of them, "Well, this complicates things." Starlight said.
"We can still take them." Rainbow said confidently.
"You guys take cover." Applejack told their fellow classmates who took cover behind a car.
"Fugitoid, guard them." Sunset ordered.
"Affirmative." The robot went over to protect their classmates.
"Let's take them!" Indigo ordered, as they engaged the ant mutants who kept crawling onto them and reproducing more.
"There's no end to these things." Fluttershy cried, as she was struggling against some of the ants.
"Well, it can't get any worse." Pinkie said.
Then as if responding to her claim, dropping in was another insect mutant that looked like a combination of a spider and a beetle, "Pinkie!" the girls shouted, as Pinkie looked sheepish.
The insect mutant chuckled, "Mm, delicious."
"What in tarnation are you?" Applejack asked in disbelief.
"You can call me Scumbug, and I see you're already acquainted with my partner Antrax." he motioned to the ant mutant and all his drones.
"We've met." Rarity said dryly.
"What do you want?" Sunset demanded.
"Our boss has us running around trying to find something to snack on, and I think we found perfect candidates."
"Snack on?" Fluttershy trembled.
"Sorry, but we're not on any menu." Pinkie answered, as the girls engaged the newcomer.
Scumbug flew around before releasing green immobilizing goo at them. They dodged as Rarity was looking as sick as ever by what was happening, "I'm going to vomit."
The bug mutant snickered, as he opened his butt to reveal the long mouth that started spitting webs, "Avoid the webs!" Juniper called.
As the ninja girls fought the insect mutants, Flash and the others watched from behind. The CMC were impressed the most, "Look at them go." Applebloom began.
"I didn't know Rarity could really fight like that." Sweetie Belle said in awe.
"Go, Rainbow Dash!" Scootaloo cheered.
Bonbon suddenly felt something poking at her neck, "Sandalwood, please don't hold me there!"
"I'm not doing anything." Sandalwood answered.
The group suddenly grew worried, before slowly turning around and saw more Antrax drones. The kids screamed, as Fugitoid defended them with his blasters, "Don't worry, everyone. I'll protect you!" he continued attacking, but more drones kept coming up and piled atop him.
"Fugitoid!" Flash and Micro Chips called.
Suddenly more drones surrounded the group and started piling on top of them. Their screams were heard by the ninja girls, "Guys!" Sunset called, as they tried to help, but Scumbug, Antrax, and the drones blocked them.
As the drones distracted the girls, Scumbug flew over to the other group, "Take what you can get, right?" he started webbing them up.
The ninja girls finally defeated all the drones, but saw no sign of Scumbug or for that matter their friends, "Oh, no they're gone." Twilight gasped.
"And they got away with the others too." Sunset added.
"Applebloom!" Applejack called.
"Sweetie Belle!" Rarity cried.
"I'm so sorry, I wasn't able to protect them." Fugitoid apologized.
"Don't worry, Professor, you did all you could." Sunset assured him.
"We got to find them and get them back." Sour said.
"But we need help." Starlight noted.
"Back to the lair!" Rainbow ordered, as they headed back.
Meanwhile, Scumbug and Antrax were dragging the students bound in webbing across the floor of a warehouse covered in Spider webs, "Where are we?" Scootaloo asked feeling scared.
"This is our place." Scumbug answered.
"You better let us go, or you'll be sorry!" Lyra warned him.
"Empty threats," Scumbug replied, "Besides, we promised the boss something, and we're going to deliver."
The two mutants dropped the six on the floor in front of them, before Scumbug called out to the ceiling, "Hey, boss, we're back!"
The humans looked up and saw something coming down from the ceiling via thread. Suddenly dropping before them was who else but Spider Bytez. The sight of him had the group looking more frightened than ever. Spider Bytez himself chuckled, "Excellent." he said, while gazing at the humans who hoped they would get out of this mess.