The Shadow Behind Her Eyes 4: Dark Secrets

by RainbowDash15

Rating: mature
Tags: My Little Pony: Friendship is Magic, Dark, Rainbow Dash, Other, Tragedy, Princess Celestia, Pinkie Pie, Applejack, Gore
Length: 5057

The fourth story in the series The Shadow Behind Her Eyes. Celestia realizes what losing the Mane 6 could mean, and goes to set things right. Meanwhile, a group of suspicious ponies go looking for answers.

*If you haven't read the other three stories in this series, I suggest you read those first.*

Suggested official rating: R for violence

With everything that's been going on, Applejack and Pinkie Pie get a well-deserved break from tracking down Rainbow Dash. Meanwhile, Princess Celestia has realized that the loss of the Mane 6 could cause problems in Equestria's future, and tries to set things right at all cost.
While all of that's happening, a group of ponies, knowing there's something that they aren't being told, go looking for answers.

Published 2015-05-17 20:10:01 UTC
Last updated 2015-05-17 20:10:01 UTC

Part 1: Secret Matters

WARNING: This story has been rated Mature by the author for graphic violence and gore, and disturbing themes.

THE SHADOW BEHIND HER EYES 4: DARK SECRETS

The sky was dark on the day everypony in town attended the funeral for the two fillies, Sweetie Belle and Scootaloo. It was a sad day for the whole town, but there was no pony sadder than Apple Bloom. Apple Bloom had just lost both of her best friends, both who were victim to horrible, gruesome deaths- Sweetie Belle had been nailed to a tree and a stick had been shoved through her head, and Scootaloo had been stabbed repeatedly to death.

The two coffins were levitated down the street past the crowds of silent, sad ponies. They were open coffins, allowing view of the bodies inside. They had been gently cleaned of blood, and expert doctors had sewn their wounds back together, making it nearly impossible to tell that they had once been horribly mutilated. The two filly's bodies had also been placed in their coffins in a position so that they could have just been sleeping. Several ponies, including one pony with rather curious golden eyes, stepped closer to get a better view of the bodies as they passed.

Applejack, Granny Smith, and Pinkie, with two royal guards on either side of them, were also at the funeral, Applejack and Pinkie being the only two left out of six friends. Three were dead and one was an insane psychopath who had already killed several ponies, including the two fillies, hence the presence of the guards.

Other than the Royal Guards, Princess Celestia, Applejack, and Pinkie Pie, nopony thought the situation could've been any worse, but in reality, it was. The town still didn't know about the other murders, including the murder of Princess Twilight Sparkle, but it wouldn't be long before the ponies began to suspect something. The official report for the two filly's deaths was "death by misadventure", but although the other ponies in the town knew little about the situation, it was doubtful that all of them actually believed the report, because of the Royal Guards who now patrolled the whole town day and night.

***

Several hours later, the funeral was over, the bodies buried in the cemetery. Apple Bloom had cried silently a lot during that, and Applejack's comforting hoof around her didn't seem to help at all. Applejack and Pinkie cried, too, not just for the fillies, but also for their other friends that had been killed.

As Applejack, Granny Smith, Pinkie, and Apple Bloom, accompanied by two Royal Guards, trotted for Sweet Apple Acres, they noticed many Pegasus ponies moving more dark storm clouds into the sky above Ponyville after the funeral. It was probably scheduled, Applejack thought, but it was ironic that the weather today was going to reflect the mood of how they felt.

The group of five were all heading up to the house at Sweet Apple Acres just as the first of many raindrops began to fall. A Royal Guard inside the house opened the door for them as they got to the porch, and they went inside.

When the five walked into the living room, they could all hear the rain start to come down harder, thumping on the roof of the house loudly. Apple Bloom headed straight for the stairs to go to her room, the Royal Guards moved into a corner of the room, trying not to be a disturbance, and Applejack went over to the couch which she flung herself upon. Next, Granny Smith sat down in her chair, and after crying a bit more, she quickly fell asleep.

Applejack realized her big brother was nowhere in sight. Big Mac must've still been outside, coming back from the funeral. He went, but he didn't stand with us, Applejack reasoned with herself. She knew he'd be in in a few minutes; looking outside, she saw that it was by now nearly as dark as night and the rain had began to come down in sheets, despite the fact that the storm had only started five minutes before.

Applejack heard hoofsteps rapidly coming down the stairs and she turned towards the noise, along with the Royal Guards, but it was only Apple Bloom, who went over and joined Applejack on the couch.

"Sis, ah'm scared," Apple Bloom said in a small voice. "An' shouldn't Big Mac be in by now?"

"Ah'm sure he's comin'," Applejack said, but her voice sounded unsure, even to her own ears.

***

Rainbow Dash, shivering and cold, flew crazily through the rain and wind, looking for shelter. Her fur was completely soaked and all the blood she had gotten on herself several days before was all washed away.

Despite the dark and heavy rain, the Pegasus kept searching, and finally spotted an old shack on the ground below, which she instantly flew for.

Stepping inside the shack, she instantly felt the rain stop pounding on herself and heard it patter on the roof instead. It was dark inside the small shack, with the only light coming from the doorway, and the whole shack smelled of moldy, damp wood. But it didn't matter.

Rainbow Dash laid down near the center of the shack and tried to sleep, but she couldn't. When she looked up again, she was horrified, but not surprised, to see some familiar faces standing in front of her- or what was left of them.

Rarity was in the front, and she advanced on Rainbow Dash as the Pegasus scrambled up in terror. Rarity' once-white coat was now rotting and streaked with blood. A hatchet wound in her stomach was spilling what was left of her putrid insides. The slash in her throat was wide and gaping, allowing an unattractive view of the inside of her neck.

"This is for Twilight," the dead unicorn snarled in a throaty voice, and attacked. Rainbow kicked at Rarity and she went sprawling across the floor, but Fluttershy was right there to take her place, her mutilated head spilling brains, her once bright-yellow coat now dirty and matted down with blood.

"The others are going to kill you for what you did, Rainbow," Fluttershy said in a chillingly calm voice, and flew at Rainbow, who managed to knock the dead Pegasus down, not even aware that she was screaming at the top of her lungs as she did so.

As Rainbow backed away from Rarity and Fluttershy, who were getting up again, Twilight herself stepped forward, the dead alicorn's body rotting away, the eye that had been stabbed with the knife now running down her face. She snarled at Rainbow and flew right at her, and Rainbow covered her head, closed her eyes, and screamed and screamed until she could scream no more. After what seemed like hours, she looked up again, right as lightning flashed. She was all alone in the shack, the horrible visions finally gone. Rainbow began laughing hysterically, but it was no more than a whisper of a sound, as her throat was raw from screaming. She tasted blood in her mouth.

After a few minutes, Rainbow closed her eyes, trying to sleep, but the nightmares haunted her, stalking the wasteland that had once been her mind.

***

It had scared everyone when Big Mac burst through the front door of the house, soaking wet from the rain, and the Royal Guard near the door had managed to turn his head in time so that instead of the bolt of energy from his horn blowing Big Mac's head off, it missed him by inches, flying out the front door into the rain.

"Big Mac! Where have ya been?" Applejack said angrily, running over to him while the guard who had nearly hit him stuttered endless apologies which were largely ignored.

"Had to finish a few trees," Big Mac said calmly.

Applejack clapped a hoof to her face in frustration.

"So that's why you were late inside? Ya get back from a funeral, see that it's starting to rain, and you go finish yer work?"

"Eeyup."

"Big Mac... Ah though... Ah thought you'd been..."

Applejack couldn't finish the sentence, and instead hugged her brother, silently thanking Celestia he was alright. When she stepped away from him, she led him into the living room and spoke.

"Well... We're all here now... We're all safe."

With those words, they all went back to remembering their dead friends.

***

Princess Celestia had arrived back in Canterlot, and as soon as she got to the castle, she stopped to levitate a rather large box into the air. Done with that, she proceeded to go down into the farthest depths of the castle, down so deep that few in all of Equestria knew that this part of the castle existed.

As she continued down, she felt her magic dampen slightly; the spell she had cast on this place to keep ponies from using magic or flying was strong, but being the one who had cast the spell, she mostly had power over it. Nevertheless, levitating the box was a bit more of a struggle.

Finally, Celestia made it to a small wooden door, which she pushed open and walked inside, slightly out of breath, but she instantly felt her magic return to her.

Looking around, she saw the familiar large, shadowy room with the familiar giant machine with tubes running from it, with the familiar buttons on it. She saw the shelf against the far right wall that was stacked from floor-to-ceiling with books on magic and magic potions. Then she saw the familiar five unicorns dressed in black coats and gas masks, making their identity impossible to determine; even their horns were covered, wrapped in black cloth. One of these unicorns walked over to Princess Celestia.

"Yes, Princess?" he asked.

Celestia sighed and gently set the large box down in front of her.

"Shadow, I know that this room was created for many things. But now, I'm going to have to ask you to do the hardest thing yet."

"And what would that be, Princess?" Shadow asked cautiously.

Celestia's horn glowed, and the lid on the box opened.

"I... I need you to fix this."

Shadow stepped forward and looked inside of the box, and although it was impossible to see the expression on his face, Celestia heard it in his voice.

"But Princess... How...? A-are you sure...?"

Celestia closed her eyes and spoke.

I'm sorry to have to ask you to do this. But Twilight Sparkle and her friends were never supposed to die. With them gone, all of Equestria is in great danger. I really don't want to ask you do do this, but I must. So I repeat: Could you please fix this? Oh, and one more thing, I will be bringing in the other two soon."

Shadow contemplated for a moment, looking at the dead purple alicorn inside of the box. After a moment, he sighed.

"Alright, Princess. I'll see what we can do."

***

While all that was happening, an angry golden-eyed unicorn was addressing four of his friends inside of his house.

"If Princess Celestia thinks she can hide what is going on from us, she is sadly mistaken," the unicorn with the golden eyes addressed his four friends, also unicorns.

"Something is going on, and we aren't being told what. Two ponies, killed? Several others, missing? Royal Guards, patrolling our town day and night? Stuff like that doesn't just happen in Ponyville."

He narrowed his eyes, silently daring his friends to challenge what he had said.

"Well, what do you think it is?" one of his friends asked.

"If you want my opinion," the golden-eyed unicorn said, "I think that those ponies didn't die by misadventure. No, no, something killed them."

"Why do you think that?" another one of his friends asked.

The golden-eyed pony clapped a hoof to his face in frustration.

"First of all, why else would there be royal guards patrolling the town? And second of all, did you look at those two filly's bodies at the funeral? The orange one, Scootaloo, had been stabbed, repeatedly. With Sweetie... the stitches suggested something had been forced through her head."

"But why would anypony do that?" the third friend asked. "I can't think of anypony in town who would do something as sick as that."

"That is exactly what we are going to find out," the golden-eyed unicorn said. And we're going to start by asking Princess Twilight. She must know something about all of this."

"I doubt she'd tell us anything," the fourth friend said. "If Celestia wants to keep the news of a killer quiet, she would've warned Twilight not to tell anypony."

"But that's just it, isn't it!" the golden-eyed unicorn said. "Why would Celestia want to keep news of a killer quiet? Wouldn't she address the whole town then to warn them of the danger? No, no, there's something bigger going on here. And we will find out what. And we are going to pay a visit to our local princess."

Part 2: Massacre

PART 2: MASSACRE

Shadow nervously looked at the three bodies lined up before him, along with his other unicorn companions. Celestia stood by, watching anxiously.

"I don't even know if we'll be able to do this, princess," he said nervously. "As far as I know, nothing like this has ever been attempted in the history of ponykind. This is almost... well, dark magic. Bringing ponies back to life would be considered by many to be... eh... unnatural."

Celestia closed her eyes.

"I do not like this anymore than you do. But it must be done. Our very future depends on it. If the Elements of Harmony are destroyed, we've lost our most important defense."

With those words, she trotted out of the dark room and began heading back up towards the castle. As she did, she spoke to Twilight, and to her dead friends, wherever they were.

"I am so sorry... this never should've happened. I am so sorry, Twilight, my most faithful student. I should've seen this coming... but I didn't... And I'm sorry I am forcing you and your other friends back to life... but it is for the best. If you can hear me, please believe what I am saying... I hope you can forgive me... all three of you."

With that let out, Celestia walked the rest of the way up in silence.

***

"Now, look," Shadow said to his companions after Celestia had left the room. As you know, it is our mission to bring these three ponies back to life. We will start with Princess Twilight. It may prove impossible to, some of you may not even want to. I know I don't. It's just unnatural..."

Realizing he was getting off topic, Shadow quickly continued.

"The fate of Equestria itself could depend on whether we succeed or fail. And don't get any ideas. This will definitely be the hardest thing we've ever attempted, so you better not expect this to be easy. As you can see, the yellow one- Fluttershy- has taken a serious blow to the head, and there is serious brain damage. This may be very hard, or even impossible to fix. But we'll cross that bridge when we get there. Anyways, we need to get to work on Princess Twilight. There is no time to lose."

While the other unicorns ran around, making settings on the machine in the center of the room and collecting potions, Shadow inspected the body itself. The alicorn had a huge slash in her side, and the eye that had been stabbed was rotting out already. Oh, this was not going to be fun.

Shadow levitated Twilight's body back-first onto the table and grabbed a scalpel. Starting where Twilight had been slashed in the side, he made the cut wider and carefully pulled the two flaps of skin apart, looking at the inside of her body. As he suspected, there was a large amount of internal bleeding, and some of the alicorn's insides had been nicked by the knife that had slashed her in the first place.

"You," Shadow said, motioning to one of his companions. Get me a tube and a bucket. I'll need to clean the blood out from inside her... but I'll need to drain the rest of it from her body first."

The unicorn brought over the tube and bucket without a word. Using the scalpel, Shadow made a slash in Twilight's neck, inserted the tube, and placed the other end in the bucket.

Using his magic, Shadow forced the remaining blood in Twilight's body to pump through it, through the tube, and right into the bucket. It took awhile, but after about fifteen minutes, the flow finally stopped, and the rest of the blood dripped into the bucket.

"Now for the fun part," Shadow murmured to himself. Taking the scalpel again, he sliced down the alicorn's stomach and carefully pulled the skin apart. Then, using the scalpel, he carefully began to cut out Twilight's innards, one by one, placing them in a neat line on the table for cleaning- intestines, heart, lungs, stomach, everything.

Finally, done with that, he began to clean the organs themselves. He started with the stomach, which he first started off by using magic to pump it. Stomach acid, half-digested food, and blood sprayed out, but Shadow continued until the stomach was empty.

Some time later, while Shadow was cleaning Twilight's liver, and a few of the other unicorns were working on the intestines, Celestia entered the room again to check on their progress. Her expression turned a bit sick when she saw what was going on.

"Is... is that necessary?" she asked, looking at Twilight's gutted body.

"This is the first step, princess," Shadow said. "It is essential that all organs be cleaned and repaired before attempting reanimation."

"Well... if you say so," Celestia said.

Behind his mask, Shadow smiled.

"Don't worry, Princess. I'm sure we can get Princess Twilight back in no time." I just hope it works.

***

Back in Ponyville, the unicorn with the golden eyes, his four friends, and several others were headed for Twilight's treehouse after it had finally stopped raining. Along the way, they stopped to get other ponies that they knew.

Going up to one house, the golden-eyed unicorn knocked on the door and waited impatiently for the stallion who lived there to answer, along with his four friends and the seven others they had picked up along the way- four mares and three other stallions.

After a few seconds, the stallion who lived in the house opened his door. Seeing the golden-eyed unicorn and recognizing him, he started to greet him warmly, but the unicorn on the porch held up a hoof to stop.

"I'm sorry. We can't talk today. We are heading to the princess's house to find out what's really going on in this town."

After explaining everything, the stallion in the house gladly went along with the group. Now thirteen members strong, they began to head over to the treehouse where Twilight lived, visible just down the next street.

***

It had finally stopped raining, and Rainbow Dash cautiously peeked out the door of the shack she was in, making sure that it was safe to go out. The visions earlier had given her an idea.

Where else would Twilight's friends be besides her own house? Yes, Rainbow thought, the alicorn's house would be the very last place they'd expect her to look for them.

But, Rainbow thought, If only i could get there first take them by surprise kill them kill them KILL THEM KIIIILLLL THEM-

Rainbow took off, flying in the direction of Ponyville, laughing.

They think they'll get me but oh no no no no i'll get them first, swear i'll kill them ALL FIRST...

After a few minutes, the pegasus flew down towards Twilight's treehouse which was now visible, and as she looked down, she saw ten or so other ponies approaching the tree house down on the ground.

It's a trap or guards or something but i'll kill them too just gotta be careful, be careful-

Rainbow flew around to the back of the treehouse and entered inside through Twilight's bedroom. As she did this, she drew a long, sharp knife that she had been keeping hidden in her messy mane. Then, grinning crazily, she listened as the group of ponies began knocking on the library door downstairs.

***

After what seemed like forever, Shadow and the other unicorns had finally finished putting Twilight's innards back inside, taking painstaking efforts to make sure they were perfect. Done with that, Shadow began to stitch the two slashes in the alicorn's body back together, using a special type of thread that made the cuts nearly invisible.

After the cuts had been stitched, Shadow looked at Twilight's face, at the two eyes that still stared blankly up, staring at everything but seeing nothing. One of the unicorns had repaired her damaged eye earlier while the others had worked on her organs, and had done a very good job; one would never guessed that just hours earlier, the eye had been rotting, running down her face.

The unicorns took one last look at her body, then, satisfied, they all began to levitate the alicorn over to the machine in the center of the room. The machine had been used for many strange science experiments, nothing like this, though.

"Well... Let's start," Shadow said nervously when the body was in place.

The other unicorns nodded and got to work, taking the bucket of Twilight's blood and another tube to pump it back into her body, along with wires, tubes and strange potions from the shelf. As Twilight's blood was pumped back into her body, Shadow carefully calculated the amount of potions he needed, and used various tubes and needles to inject them into her body.

After what seemed like awhile, Twilight was looking perfect, except for the fact that she was dead.

"Are you ready to try this?" one of Shadow's companions asked him.

"It is now or never," Shadow replied. "Let's do this."

One of the other unicorns pressed several buttons on the machine and pulled a lever, and there was a sharp cracking sound and a puff of smoke, and a tube still in Twilight's body injected a carefully calculated amount of a deep black potion.

With the injection complete, the unicorns all crowded around Twilight's dead body, looking for signs of life. They saw none. The alicorn still remained unmoving.

With a sigh, Shadow used his magic to close Twilight's eyes, which were still open.

"We... we better go tell the princess," he told them.

"She will not be happy, but... we did the best we could."

The unicorns all turned and headed for the door of the room, removing their uniforms before exiting.

As they all left and the door shut behind them, Twilight's eyelids suddenly fluttered open.

***

"I'm telling you, she's not here," one of the stallions told the golden-eyed unicorn. "You've been knocking for five minutes. There is nopony home."

The golded-eyed unicorn turned to the stallion.

"I did not walk all the way across town for this," he said. "I came to get some bucking answers. And I will get some answers."

With those words, the golden-eyed unicorn used his magic to force the front door open, and the thirteen ponies went inside of the library.

"Well," one of the unicorns observed, looking around the front room. "What happened here? This place is a mess."

"You all look around here," the golden-eyed unicorn said. "I'm going to check upstairs."

With that, he ran up the staircase, up to Twilight's bedroom. It was also empty in there, or so he thought. He looked around, disappointed that nothing was there, and turned to leave. As he turned around, Rainbow Dash came out from behind the bed, flew over to him, and stabbed him in the back of the neck before he even realized what was happening.

***

After fifteen minutes of relentless searching throughout the library, the other twelve unicorns were ready to give up, having found nothing.

As they began to prepare to head out, one of the unicorns spoke.

"Didn't Truth Tracker head upstairs earlier?"

"Yeah, I think he did," one of the four mares replied. She called upstairs.

"Truth?"

There was no answer.

"I guess I'll go up and find him," one of the stallions volunteered. He began to trot upstairs while the others watched. As he reached the top, however, something flew out and knocked into him, and the stallion tumbled back downstairs, and there were crunching sounds as his neck and spine broke. He didn't even have time to scream.

The thing that had knocked the stallion down landed in front of the eleven remaining shocked ponies.

"You thought you all could trick me," Rainbow Dash giggled. "Bet you weren't expecting me to make the first move! I know you were sent to kill me. But I'll kill you all, too!"

Suddenly, the sharp knife was in Rainbow's hoof, and before any of the ponies could react, there was a huge spray of blood as Rainbow flew right through them, the knife finding the neck of one of the ponies. The pony, a mare, gasped and tumbled to the ground, but Rainbow had already stabbed two more to death before the first pony had bled out. By now, the other ponies were in a panic, trying to stop the crazy pegasus, or run away. One of the ponies made it out the front door, which Rainbow didn't notice, but she had clearly seen the other ponies, trying to find a way to escape, running all around the library.

A bolt of energy flew past Rainbow's face, and she flew over to the unicorn that had shot it, and rammed the knife into his eye. Two other ponies ran for the front door, but Rainbow flew in between them, opening up their stomachs as she did so, and they screamed and fell, spilling a ton of innards and blood onto the floor.

The remaining four ponies, all earth ponies, were huddled in a corner of the library, shaking with fear as Rainbow Dash stalked over, grinning madly. One slash, and one of the ponies was quite dead, and Rainbow was sprayed with her blood. One stab, and another pony's insides spilled out as his stomach was unzipped. Two more stabs, and the last two ponies were dead, having each been stabbed through their throats, and blood gushed out in a horizontal curtain from the wounds.

Rainbow Dash wrenched the knife out of the last pony's neck and looked around at the carnage. None of these ponies were Applejack or Pinkie Pie. It had all been a trap set up to kill her.

But it didn't work oh no, it didn't, and now i'll find them and kill them instead-

Rainbow laughed, stuck the knife back in her mane, and flew right out the front door of the library and into the still-cloudy sky.

***

Later that day, all of the ponies in Ponyville, except Applejack, Pinkie Pie, and the Guards who patrolled the town, were all gathered around in the center of Ponyville, listening to Mayor Mare as she finished explaining everything to the ponies, having been told earlier by the lone survivor of Rainbow's slaughter in the library. She had sent her advisors around the town to notify all of the ponies, except the Royal Guard patrols, of the meeting.

"Now, I still don't fully understand the whole situation," the mayor continued, "but you must take caution. We don't know where Rainbow Dash is, or where she might go next. We have reason to believe that she killed Princess Twilight and several others. It is of utmost-"

Before she could finish speaking, a carriage, being flown by four Royal Guards, flew down and landed in front of the crowd of ponies. A Guard inside of the carriage got out and stood in front of Mayor Mare.

"You are telling these ponies classified information," the Guard said sternly. "This information was being held to protect the citizens of this town. I must ask you to stop at once."

The mayor cowered a bit from the icy gaze but kept her composure.

"Y-you were not protecting anyone. You were putting them in even bigger danger-"

"That would be for Celestia to decide," the Guard said. "Step down."

As the mayor stepped away, the crowd of ponies, who had heard everything, started talking amongst themselves. At that moment, the Royal Guards who patrolled Ponyville turned down off of a street, saw the crowd and the other guards, and rushed over to find out what had happened. As the newly-arrived Guards began to explain to the patrol captain, one of the ponies in the crowd called out angrily.

"How could you have not told us about this? Because of you, my friend is dead!"

The Royal Guard turned and spoke out to the crowd.

"We only held this information so we could protect you from-"

"But you didn't protect us, did you?" the voice called. "Because of you, more of us got killed!"

This statement was followed by the whole crowd shouting angrily and booing at the Guards.

The newly-arrived Guard and the patrol captain trotted some distance away, turned towards each other and talked, even as the ponies in the background kept shouting furiously at them.

"This isn't good," the new Guard said. "They all know what's going on now."

"It's going to be a lot harder to protect these ponies now that they know what's going on," the patrol captain agreed.

"We'll just have to be ready, I guess. We must stop Rainbow Dash at all costs. There's a storm coming. And I have a feeling it's going to be a lot worse than the one we had earlier."

The two guards looked away and up into the sky, where the sun was still being blocked by dark clouds.

Author's Note

I'm sorry this took so long. That's all I have to say. Hope you can forgive me.