Equestria Ninjas: Friendship School

by Wildcard25


Shini's Nightmare

On board the Technodrome, the Dark Turtles and the Purple Nightmares were sparring, as Shredder paced around grumbling, "We've been here for weeks and we still don't have an alternate power source to power the portal!"

Chrysalis approached, "And it's all because of Princess Twilight, her friends, and the ninjas."

"Hey, do we really need the portal anyway?" Dark Raph asked.

"Yeah. We can take them on just fine." Dark Mikey agreed.

"Given your previous failures it's hard for us to believe that." Shredder noted, making Night Terror and his gang chuckle.

Chrysalis flew into the Purple Nightmares faces, "You find this amusing, Night Terror? Don't forget, you and your gang haven't been so successful yourselves."

The Dark Turtles laughed at the Purple Nightmares, only for Chrysalis to turn to them frowning which shut them up.

The doors opened, and Krang walked in, "I have exciting news, everyone!" he cackled.

"Speak, Krang." Shredder said.

"I have finally found us a fuel source to use for the portal, and it's right in the Crystal Empire."

"The Crystal Empire?" Night Terror asked.

"That was where we had our trial run." Dark Leo remembered.

"Precisely. You fought the turtles and their allies down in the Crystal Catacombs. And now you will be going back there." the alien brain explained.

"And what are we looking for?" A purple nightmare asked.

"Sombra Crystals." Krang answered.

"We used those to trap the ninjas in." Dark Donnie recalled.

"Correct. And now you must go back to the catacombs and retrieve a potent amount for us." the warlord informed.

"Both teams will be on this mission." Shredder instructed the Dark Turtles and Purple Nightmares.

"So all of you work together, otherwise the punishment will be severe." Chrysalis warned them.

"As you wish." they bowed their heads.

"Then take the module and get going! Shredder ordered, as the two teams took their leave.


Meanwhile at Twilight's castle, Twilight, her friends, and the ninjas were in the throne room looking at the map. Hovering above the Crystal Empire were the cutie marks of Sunset Shimmer, Shinigami, and Fugitoid.

"Wow. The map's calling us?" Sunset Shimmer asked in disbelief.

"Well, you had to know it was coming," Pinkie noted, "I mean the others had their shot at a friendship mission."

"When you put it that way it sounds logical." Shini admitted.

"How exciting to be called by the map." Fugitoid said all giddy.

"Though what could be going on in the Crystal Empire that needs our attention?" Sunset Shimmer wondered.

"We're not sure, but I'm sure you'll figure it out when you get there." Twilight answered.

"In that case I suggest we leave at once." Fugitoid recommended.

"Agreed." Sunset Shimmer nodded, as the three headed for the train station.


Later on once the trio reached the Crystal Empire, Shini spoke up, "So where should we start first?"

"Our best bet is the castle." Fugitoid suggested.

"Yeah. We'll work around from there." Sunset agreed, as they entered the empire, before seeing a familiar Pillar galloping over to them.

"Oh, thank goodness you're here." Mistmane said in relief.

"Mistmane, what's wrong?" Shini asked.

"There's trouble in the empire. Or rather under the empire." she explained.

"What do you mean?" Sunset asked.

Mistmane explained, "I spotted the ones you call the Dark Turtles and the Purple Nightmares heading into the Crystal Catacombs."

"Goodness, why would they be going down there?" Fugitoid wondered.

"We're not sure, but we have to find out." Mistmane said.

"Then let's get going." Sunset Shimmer said, as the three followed the pillar to the entrance of the catacombs.


Meanwhile below the Crystal Empire, the two villainous teams were mining for Sombra crystals, "Remember we need to bring back a large potent supply." Night Terror instructed the group.

"Yeah-yeah, we know." Dark Raph grumbled, as he was filling a sack full of the crystals.

"You think after we succeed our bosses might consider giving us a bonus?" one of the Purple Nightmares asked.

"With all we've been putting up with? We better." another member answered.

"Think we got enough bags yet?" Dark Mikey asked around.

"Looks like enough." Dark Leo counted.

"Yes. Plenty. Let's get back to the module." Night Terror was about to walk away only for a kunai to nail the wall close to him.

The villains looked over to see the four ponies standing in the tunnel's entrance, "You're not going anywhere." Sunset Shimmer warned them.

"Oh, crud." Night Terror groaned.

"Alright, where's Leonardo and the others?" Dark Leo inquired.

"I'm afraid they aren't here right now." Fugitoid answered.

"You mean it's just you four?" Dark Donnie asked.

"Um, yes." Shini answered.

"Then this should be easy." Night Terror said, as they armed themselves.

"I think you'll find we're more than a match for all of you." Mistmane warned them.

"Take them!" Dark Leo ordered, as the groups went on the attack.

Shini and Sunset used their ninjitsu moves to disarm some of the Purple Nightmares, until the Dark Turtles were going to pull a sneak attack, "Girls, heads up!" Fugitoid called, as he shifted into anthro mode and released his blasters and started shooting at the evil clones.

"Stupid scrap heap!" Dark Donnie cursed, as the clones tried to deflect his shots.

Mistmane was blasting at the two groups with her own magic, until the enemies came together and started fighting back. Soon they were at a stalemate, as Sunset called to them, "What're you doing with all those Sombra crystals?"

"They're going to help us conquer this dimension." Dark Donnie answered.

"Shredder and Krang must be planning to use them as a fuel source to power their portal." Fugitoid realized.

"Yeah. Them and Chrysalis, of course." Dark Mikey added, surprising his brothers.

"Wait. Chrysalis? She's involved in this?" Sunset Shimmer asked.

"Always has been," Dark Mikey continued to spill the beans, "She was the one who cloned us the same way she cloned Princess Twilight and her friends during their camping trip."

Dark Raph smacked Dark Mikey to the ground, "Shut it, big mouth!"

"So Chrysalis is in league with Krang and Shredder." Shini gasped.

"Correct," Night Terror confirmed, "Of course, you won't be able to stop them from opening a portal to Dimension X."

"Try us." Fugitoid challenged them,as they prepared themselves for another fight.

"Actually, we're on a schedule so we have no time to deal with you." Dark Leo answered.

"So how about you enjoy a little nightmare or two?" Night Terror tossed some nightmare crystals at the four.

Mistmane was able to repel one of the crystals about to collide with her, but Fugitoid, Sunset, and Shini ended up getting hit in the head with a crystal each causing their eyes to glow green before collapsing.

"No!" Mistmane cried.

"Adios, losers!" Dark Mikey cackled, as the villains ran down a tunnel carrying their bags of crystals.

Mistmane looked down at the three in concern, "This is bad. I have to wake them up." Mistmane used her magic on Sunset and Fugitoid causing them to regain consciousness.

"Oh, dear." Fugitoid gasped.

"That was horrible." Sunset gasped.

"What happened?" Mistmane asked.

"I was at Canterlot high with all the students and my friends all shunning me and fearing me the same was they did when Wallflower used the memory stone to erase their good memories of me," Sunset began while feeling sad, "I never want to feel that again."

"I was reliving the horrible memories of when I sold Subprime the black hole generator, and watched the Triceratons planet and earth get destroyed with the everyone blaming me." Fugitoid added sounding guilty.

"The Sombra crystals can cause nightmare hallucinations," Mistmane explained, "Now we must wake Shinigami and catch up with our enemies." Mistmane tried to use her magic to bring Shini back, but it didn't work.

"Nothing happened." Fugitoid noted.

"Why didn't it work?" Sunset asked the old pony.

"I'm afraid the nightmare in her is stronger than it was in yours. My magic can't bring her out." Mistmane explained in worry.

"So we can't do anything?" Fugitoid asked.

"You two go after them. I'll stay with Shini." Mistmane instructed.

And so Sunset and Fugitoid followed the tunnel to catch up with the Dark Turtles and the Purple Nightmares. Mistmane looked down at Shini in concern wondering what she was dealing with.


Inside the witch girls mind. Shini as her human form was wandering the streets of Japan before looking over and saw herself as a child, and her adopted father, "What?" she asked herself as she followed them, before realizing what was happening, "Oh, no. Not this!"

She watched as the Yakuza surrounded them, as her father told her to hide leaving him to deal with the mob, but sacrificed himself, "Daddy!" Young Shini cried.

"No!" Shinigami cried, as the memory faded, leaving her in the darkness and on her knees crying, "Father."

"Painful, isn't it?" came a voice that sounded like Shini's.

Shini looked up and saw a dark spectral version of herself standing before her, "Losing your parent. Having no one around to help you. But then again you never did have anyone before then." the specter explained, as Shini recalled her time at the orphanage and how the kids treated her.

Watching the painful memory made Shini even sadder, "Please, no!" she pleaded for it to stop.

"No one was there for you then, and no one is here for you now."

"That's not true!" Shini cried, "My friends are with me."

"Really? Where are they?" the specter asked, as they looked around, "No one is here but us. They left and abandoned you, Shinigami. They never cared about you."

Shini looked around seeing all her friends standing before her, but had looks of disappointment on their faces before fading away, "No! Please! Don't leave me!" she pleaded with her friends.

"The pain can go away, you just need to give into the darkness in your heart. Be the person you were always meant to be." the specter offered her hand to Shini who looked at the hand in concern.


Meanwhile, Fugitoid and Sunset were following the trail of hoof prints, before spotting them up ahead, "There they are." Fugitoid spotted them.

"We can't let them get away!" Sunset called, as she teleported the two before the groups.

"No way!" Dark Leo gasped.

"How did you get free from your nightmares?" Night Terror asked in confusion.

"We had help from a friend." Fugitoid answered.

"You better hope you'll still have help when we're through with you." a Purple Nightmare said, as the groups fought the two.


Back in Shini's mind, the girl continued to look at the specter's hand, "Go on. And I'll make sure you're never weak and alone again." it tempted her.

Shini still feeling unsure, but too drawn by the specter's voice reached out, but before she could clasp with the specter's hand, another hand reached out and grabbed her wrist surprising the two.

"Hold up there, kiddo." came a familiar voice. Shini looked and saw it was her late father standing by her side.

"Father?" Shini gasped at the sight of him.

The specter spoke to him, "We don't need you anymore, old man."

Shini's dad answered her, "Tough. You stirred up my memory. Now you're stuck with me." he turned and showed Shini more happy memories.

Shini watched as her past self and her dad were training in ninjitsu, "Remember all I taught you, Shinigami." her father old the younger Shini.

"Yes, daddy." the child answered, as she blocked some of her fathers moves, before sliding under his legs and kicked his back making him fall forward.

"Good." he said.

"I remember this." Shinigami said in surprise.

"Yes. I trained you in the art of ninjitsu so that you could defend yourself." her father's spirit explained.

The specter appeared, "Yeah, but a lot of good that did. The Yakuza took his life, left us alone with nothing."

"Her, not you," Shini's father told the specter, "Shini, I understand you still carry the burden of growing up without me and the problems you had at the orphanage, but those days are behind you. Look at all you accomplished because of my teachings."

Shini saw more memories flash before her eyes, from joining Karai's Foot Clan, becoming an allie to the Turtles, and their friends, helping the Rainbooms defend Camp Everfree and New York, saving Equestria from Dark Codex and the Storm King, and having fun with Mikey, "You have friends and a new family, and they will never abandon you so long as you believe in them. Just like I always do."

Shini watched the memories as her hope was restored, "You're right. My friends would never give up on me. Just as I never do on them."

"You're making a big mistake." the specter warned her.

Shini turned to her specter looking angry, "The only mistake I've made was listening to you!" she punched the specter making it disperse.

"That's my girl." her father crossed his arms proudly.

"Thank you so much, father." Shini hugged the old man.

"My pleasure. But now it's time for you to go."

"What? No, I won't lose you again."

"You can never lose me, child. And besides I'm much closer than you think." he said, before dispersing into light, and suddenly Shinigami woke up with a gasp.

"Are you ok, Shini?" Mistmane asked in concern.

"I'm ok. Where are Sunset and the professor?"

"I sent them ahead to stop the Dark Turtles and Purple Nightmares."

"They'll need help. We have to hurry." Shini ordered, as the two hurried to catch up to them.


Back with Sunset and Fugitoid they were holding their own against their enemies, but were starting to get overwhelmed by their strength and numbers.

"Man, we could really use some help right now." Sunset groaned, as she was using a kunai to block a knife being wielded by a Purple Nightmare.

Suddenly the Purple Nightmare was nailed with a familiar gold ball, and the two looked over seeing Shini and Mistmane, "What took you so long?" Fugitoid asked, as he dodged Dark Raph from hitting him.

"I needed to overcome my nightmares." Shini answered, as she and Mistmane joined the fight taking some of the slack off their friends.

"Hey, dudes, I found the module!" Dark Mikey called down another tunnel.

"Hurry!" Dark Leo ordered, as the groups made a run for it.

"Don't let them get away!" Sunset called, as the four chased after them.

As the groups were reaching the module, Sunset had one last trick to pull and used her magic to send four kunai in their directions and cut the bags of four sacks causing the Sombra crystals to spill out.

"No, the crystals!" a Purple Nightmare cried, as they tried to go back for them.

"Leave them, or we'll be captured." Night Terror ordered, as they piled into the module that took off underground that filled up with lava.

"They escaped." Mistmane sighed.

"Yes, but they didn't get all the crystals they planned to get." Fugitoid noted.

"At least it's one victory." Sunset added.

"Actually, I've had my victory already." Shini smiled.

"Huh?" Sunset and Fugitoid asked.

"I'll tell you when we get up top." she explained.


Back at the Technodrome, the groups presented themselves before the villains, as Chrysalis shouted at Dark Mikey, "What were you thinking blabbing about me to them?"

"What, they were going to find out anyway weren't they?" Mikey's dark clone asked, only for Chrysalis to grit her teeth at him.

"And what's worse, you lost a good helping of Sombra crystals." Shredder scolded them.

"Well, we did salvage two sacks." Night Terror showed them.

Shredder sighed, until Krang spoke up, "Actually, this may be all we need to fully power the portal. So their mishap wasn't a total loss. You all did well."

"Thank you, boss." Night Terror bowed his head.

Krang snickered, "Soon those miserable turtles and ponies will cower before us all!" he laughed hysterically.


Later on, Shini was telling the others about what she had to go through in her mind, "I can't believe you faced your problems head on." Fugitoid gasped.

"Well, I had help." Shini admitted, while recalling her father.

"We're proud of you, Shini," Sunset said, "I'm sure your dad would be proud too."

"Trust me. I already know." Shini assured, as their cutie marks started glowing.

"I guess it's our time to go." Fugitoid said.

"Have a safe journey back to Ponyville, you all." Mistmane bid them a farewell.

As the three walked for the train station, Shini thought to herself, 'Father, thank you so much.'

In the human world on the continent of Japan, a figure was standing before a headstone in a cemetery. The figure was decked out in a cloak and bamboo hat looking down at the headstone reading 'Ancient One'. The figure lifted his had up a bit to reveal it was Shini's father.

"Shinigami, one day you will understand why I had to disappear." and with that he left the cemetery.


Back in Equestria as it was getting late, Twilight and the others were in the castle lounge room listening to what Sunset, Shini, and Fugitoid learned.

"You mean to tell us, Chrysalis cloned the six of us that day during our camping trip?" Applejack asked in disbelief.

"Straight from Dark Mikey's mouth." Shini confirmed.

"Well, now everything about that day makes sense," Twilight realized, "She was trying to tear us apart."

"Sounds like there's more to it," Starlight noted, "I mean, she cloned you girls, but not me."

Twilight realized, "I got it. She wanted our clones to learn to whereabouts of the Tree of Harmony so she could use them herself."

"But the elements are still there." Rarity recalled.

"So she must've failed somehow." Donnie said.

"Well, now we know where our dark halves really came from." Raph said.

"And now it's more important than ever we stop Krang, Shredder, Chrysalis, our dark selves, and the Purple Nightmares." Leo declared.

Suddenly a portal appeared out of nowhere, "What's going on?" Fluttershy asked in concern.

"Where's that portal coming from?" April wondered.

Stepping out from the portal were four figures, that the ninjas recognized. It was the turtles from their other dimension who had also taken the form of ponies. Unlike the first time they came to Equestria, they had become mutant ponies.

"Leonardo?" Leo asked in confusion.

"Guys?" Sunset, Twilight, and Spike asked.

Leonardo spoke to them seriously, "We have to talk."