Secret Phantoms and Secret Pains

by HAZESHIFT

Rating: teen
Tags: Princess Celestia, Crossover, Tragedy, Main 6, My Little Pony: Friendship is Magic, Dark, Sad, Princess Luna, Princess Cadance, Adventure, Shining Armor
Length: 4411

The rogue Queen Chrysalis is back and wielding a power that threatens Equestria. While others want to begin preparing troops, Shining Armor has a different idea, one kept secret for a long time, something about the greatest soldier to ever live.

The changelings lead by the rogue Queen Chrysalis are back and wielding a new power that threatens Equestria. While other want to begin preparing troops, Shining Armor has a different idea. an idea he's kept secret form every-pony for a long time. His former Commanding Officer was the greatest soldier to live on the battlefield, and for years everyone thought he was dead. Now as Equestria comes closer to possibly its darkest hour Shining will do whatever it takes to save Equestria

A Metal Gear Solid 5: The Phantom Pain crossover
coverart by InkieHeart

Published 2015-10-29 18:20:01 UTC
Last updated 2015-10-29 18:20:01 UTC

Chapter 1: His Biggest Secret

Chapter 1: His Biggest Secret

The whole room was tense. Normally the throne room of Canterlot Castle could normally been seen as a calm quite place where both Princess Celestia and Princess Luna ruled the country of Equestria. But today was not normal, tables lined the length of the room and each was filled with ponies sitting on them. On each table piles of papers, charts , and maps were spread out and being looked over by everyone in the room. The raucous all the ponies seemed deafening until the throne room doors swung open and everything went silent. Each pony got up and Saluted as Princess Celestia and Princess Luna walked in, making their way to their raised seats. Behind them came Princess Mi Amore Cadenza and Prince Shining Armor, who had rushed from the Crystal Empire to attend this meeting. And after them came the Elements of Harmony led by Princess Twilight Sparkle.

All the ponies held their salutes until the last of the Elements had taken their seats. The only sound was the sound of many hooves hitting the ground and after that there was silence as the ponies waited for one of their Princesses to speak. Celestia looked at all the ponies in the and she could tell they were tired. Some had bags under their eyes, some of their manes were frayed, and other stunk just slightly. They had been in this room for at least twenty four hours discussing something she deeply deeply wished she would have never talked about again. War.

“At ease my faithful guards” she smiled as best she could, thought the topic she was going to discuss made it hard. “Now I know that this may be hard for many of us to handle, but Now that everypony is assembled, let us begin. Luna?” Celestia let her sister have the floor.

Luna rose from her seat, her magic glowing and the curtains of the room shutting making the room a bit darker. As it did Luna shot a beam at the floor and all watched as a map of the world sprung to life. Luna walked down from her seat and was handed some papers by a pony whom she thanked before she cleared her throat.

“Two weeks ago we received two reports. One form our embassy in the Diamond Dog Kingdom and the other form our Embassy in the Griffon kingdom. Both reports detailing the same incident. As of what we know now There was a small part of the Griffon Kingdom army doing routine training and patrols with a a part of the Diamond Dog kingdom, this was normal as they do this a couple times a year. What happened next is that apparently a large changeling force came out of nowhere and engaged both forces. We along with our Diamond Dog and Griffon allies suspect this to be the work of the rogue Queen Chrysalis,” All eyes landed on Cadence and Shining Armor when the name was spoke.

After the wedding Both of them as well as Princess Celestia and Luna had sent word to the Changeling Empire, demanding to know what was going on and had given way to this unprovoked attack. The quick response that had come from the leader of the changelings, King Metamorphosis clued them into the reasons. As it had turned out the king’s second wife, Chrysalis was sick of their station and had been pleading with the king to use their military strength to improve their place in the world. He denied her request vehemently many times, knowing that even though he knew that their transformation ability could make them stronger than their allies. Btu Many of the lands had been at peace for a long time, longer than his reign. ANd he knew that now they way to advance was to do so not with fighting but with reasoning. HE had planned to begin talks with Equestria about integrating his people in exchange for the services they could provide. But Chrysalis saw ponies as weak, creatures that gave of so much love and emotion but had few ways of using it to their advantage. She would not tolerate a relationship where the changelings she ruled were not the ruling species.

So in secret she snuck away, drawing on younger more impressionable changeling minds and swaying them to do their bidding. She promised them so much for their loyalty, an unflowing amount of love and land of their own above the surface in a place with lush and fertile vegetation unlike their home. Many were quickly swayed to her cause and in secret they left to seek their fortune and victory. Many knew the rest of the story as it led to her learning of the upcoming royal wedding, along with her capturing PRincess Cadence and brainwashing Captain Shining Armor. After the wedding though word finally got back to King Metamorphosis who swore his help to Equestria in locating his former Queen, but for months and months she eluded everyone. No one had seen nor heard about her and her forces for months.

“Do we have any confirmation that she was behind this?” Shining asked leaning forward from his position,part of him hoped whatever was going on was an accident, he was ready to fight but he had spent most of his life in peace and he knew it would be sad to see it end.

“Yes we do,” Luna’s horn glowed and a small crystal was levitated onto the table. “It was lucky that the GRiffon empire decided to start recording the joint exercises they are doing or we may have been doing nothing more than estimating what happened and we we want to do,” she said as her magic activated the crystal and a flat screen popped into existence. They are was flat and partially desolate as diamond dogs and griffons were sparring with one another and chatting amicably. For a while this scene continued until everypony in the room noticed the sky becoming less blue and more cloudy gray. Everything became more smoggy and both species stopped whatever they were doing and for a brief few seconds everything was still and quiet.

Suddenly out of a fog rolled in and screaming could be heard. Small black flashes could be heard and seen moving through the approaching fog. Order were quickly shouted out as formations were made. within a few more seconds the fog rolled into the formations of soldiers and that’s when everything began, bodies began falling, not struck or hurt but just falling, some silent and some screaming as they tried to defend themselves from whatever was happening. This continued until most of the soldiers had mysteriously disappeared and then something obstructed the view of the crystal. A changeling blocked the view looking directly into the crystal seemingly knowing it was being recorded, his appearance unnerving some of the ponies watching. His face different form the normal black of a changelings. His instead was more of a ghostly white and more gaunt giving him a skull like appearance. for a while he simply stared the screen showing his deep satre to all who were watching and then he began to laugh. A low chuckle giving way to a loud boisterous laugh that didn’t belie the madness within him. WHile he was still laughing he began to move, walking away from the crystal showing his full form. as he exited the farme all eyes of the ponies in the room came to look at his flank, where etched in his chitin was the mark of a chrysalis. After he exited the frame more changelings could be seen, all looking like the normal changelings they had seen but all of them also bore the mark of a chrysalis etched into their flanks. The video finished there the screen going dark before the screen flickered out of existence.

“We also have confirmation that no one was found at the site of the attack, dead or alive. And no sign that there had been any fatalities from either side,” Luna said her low tone doing nothing for it not to be heard by everypony in the room due to the sheer silence.

______________________________________________________________________________

Shining Armor sat in the throne room hours later, everything being moved out and the number of ponies in the room drastically reduced. The talks had gone on for a couple of hours, and he had sat listening to all the other ponies talk. Many had given the same kind of plan, They should start preparing for battle immediately. They wanted to began drumming up troops and begin stockpiling changeling wards to deploy to the borders of the country to begin holding the line just in case of an immediate attack. He agreed that they did have some merit but ultimately disagreed with just playing defense. There was still too much they didn’t know about what Chrysalis was planning and what she had done to take out the contingents of the diamond dog and griffon armies.

He sat there in the throne room with his back to a pillar watching Cadence and Twilight converse with Celestia and Luna while the other elements talked about what they had scene and wondering what he was wondering about only out loud. He knew that simply getting the troops organized and sending large formations out would only end badly. He knew that the formation work and defense that the diamond dogs and griffons could put up was second and third to none only to the Equestrians if they were not equal. But whatever weapon, magic, or trick Chrysalis was using ultimately made large troops movements ineffective if not useless. HE thought that if they ever wanted to stand a chance then the thoughts of what they were going to do were going to have to change to stealth.

SHingin looked to Cadence, he wanted to protect her and his sister more than anything, he thought back on his training and remembered how his instructor put it. “MAny say you should leave your best for last but if your best will allow you to end the conflict quicker than anything then those people are fools,”

“Everything alright PRince Armor? A voice broke him out of his memory as he turned to find that the new Captain of the Royal Guard; Tower Shield standing next to him.

“What? OH yeah everything’s fine...all the news today though just weighs on the mind and all. You know?”

“Yes sir i know. Honestly i’m probably in worse shape than you, i haven’t been in charge all that long and now i’ve got to deal with this...it’s a bit nerve racking,”

“I can understand that...can i ask you a question Tower?” SHining told him and then asked him a question, the answer of which would tell Shining if he intended to go forward with his plan.

“Of course Prince Shining, you don’t even have to ask sir,” Tower saluted making Shining chuckle, he remembered back when he first became Captain he acted the same way for awhile.

“First of you can just call me Shining, you don’t have to act so stiff How experienced and trained are the stealth units?” he noticed the wince Tower gave giving him most of the answer he kind of hoped he wouldn't get.

“To be honest si...Shining..not well at all, many of them are inexperienced, not to mention the funding for that branch has been getting reduced, despite what Princess Luna has been trying. We still have a complete information network but it’s not great seeing as how we have no veterans.

“Is that so?” Tower looked at Shining when he answered in a matter of fact tone. the smile he had was gone form his face and replaced by a look Tower had seen a few time when SHining had been captain. “Tower do you think you can give me a hoof with somethign real quick?”

“Yes Si...Shining whatever you need,” he nodded.

“Ok then first, we’re gonna need to go to your office,” he said as he put an arm around the slightly taller earth pony and walked towards the throne room doors.

____________________________________________________________________________

The walk took them several minutes but when they arrived Tower quickly opened the door. “Thanks Tower,” Shining told him as he stepped in a let a small wave of nostalgia roll over him. “I see you haven’t done any decorating yet,” He noticed that the walls were bare, devoid of the things he put on them in his tenure as Captain.

“Oh yeah, i’ve been meaning to but haven't found a good amount of time,” Tower rubbed the back of his head thinking about how lonely and bare his office was.

“You have a marefriend Tower?” Shining asked surprising the stallion. “I remember i was the same way in the beginning btu Cadence help me straighten my schedule out and suddenly i realized i had much more free time than i ever realized,”

“Really?...maybe I’ll ask her then next time i see her. She is good with planning,” TOwer said before noticing that Shing was walking in a peculiar way, almost as if he was trying to retrace his past steps. “Um Shining can I ask what we are doing here? I know you said you have a plan, but wouldn’t it be better to share it with the princesses?” he asked as Shining finally stopped moving giving a quick knock on the wall in front of him.

“I do and I will but first I need to get something very important to the plan. I left it here a very long time ago,” he told TOwer as his horn lit up and concentrated on a particular set of stones on the wall,a few runes lit up on the stones and then magically they began to pull themselves free of the wall.

“Sir, can i ask exactly why you would do that?” Tower slipped back to calling him sir mostly out of surprise that he had never known about what SHining was showing him. He watched as the stones freed themselves from the wall and then neatly stack themselves against the floor.

“Well part of it was because I was ordered to keep this hidden and a secret,” Shining a said as he reached in and pulled out a pair of saddlebags that were dusty, old and ripped in small places. “And another part was because part of me was really hoping that the time would never come when i would have to share this with anybody, not my wife, my sister and her friends, the princesses, nor any kids i would have in the future.” Tower watched as Shining opened the bags, he couldn’t see what was inside them for his position but he could tell it was something Shining Armor cared about deeply considering the look on his face. “The only reason I ever thought this would ever see the light of day again was if Equestria was on the brink of losing or if a the beginning of a threat ever appeared that I thought we couldn’t face down with what we have, That I thought the princesses and my sister and her friends weren’t capable of defeating with their powers,” He put the bags on as he replaced the stones back into the wall so as if nopony could tell that anything had moved at all. “With what we saw in that recording crystal Tower, and with what i’ve heard today i believe that this is one of those occasions,” he told Tower as he walked out and headed back to the throne room, Tower following behind him a few seconds later after getting over the shock of what SHining had told him.

As he caught up Tower swore that he he Shining Armor sigh to himself saying “Oh this is gonna be fun to explain,”
____________________________________________________________________________

As he walked back into the Throne room he noticed that some food had been brought in and that all of Twilight's friends were currently enjoying it while Celestia sat with Luna and Twilight sat with Cadence, both of them noticed him as he and Tower walked back into the room.

“Oh Shiny there you are, we were wondering where you went,” Cadence got up a walked over to him giving him a hug, the warmth from her gave him some courage for what he was about to do. “Oh what are these she said finally taking note of the saddlebags.

“Are those...your old saddlebags!?!” Twilight said in a mix of confusion and happiness. “I haven’t seen those since before you became Captain,” She said as her voice carried getting everyone’s attention. “I always wondered where they went. Did Tower Shield find them somewhere in the castle or in your old office?” She said smiling at him, he loved how naieve she could be sometimes despite being smarter than so many.

“Um no. I actually just got them from the hiding place i put them in the wall of my old office,” Shining said, deciding not to give riddles or try to beat around the bush, talking with Applejack at his wedding had taught him better. He noticed after he said it that Celestia was now giving him her full attention as she stood, making her way down from her throne with Luna right behind her. “And if you want to know why...well...it’s because I was ordered to,” he never broke eye contact with Celestia while he said that, watching as her serene small smile turned into a less friendly frown.

“but why would Princess Celestia order you to-”

“Princess Celestia never ordered me to do it Twilight, she doesn’t even know that this existed, It was an order from my former Commanding Officer,” he interrupted Twilight’s question while trying his best not to crack under pressure from the aura Celestia was now giving off.

“Shining Armor,” Everyone looked at Princess Celestia when she spoke, noticing her tone and stare she leveled at Shining Armor. “What is in the bag?” she asked, but to everyone who heard it did not sound like a question, more like a demand.

“Our plan Princess. I listened to all the others talk about how we should defend ourselves. But I know it’s not going to work, and you should also know that. What ever Chrysalis has it has the power to decimate armies without a fight...so i know that instead of sending in troops we’re going to need to be...more covert. And in talking with Tower i know we don’t have anyone capable of doing what we need,”

“Shining i don’t know what you-” Celestia started but her sister jumped in ahead of her.

“Hold on sister I wish to hear what he has to say,” Celestia calmed herself down, although if Shining was headed where she thought he was headed then it would be hard to stay calm.

“Thank you Princess Luna. Can I ask about how much you read up on our military history since your return?”

“I have tried to read up on absolutely everything i can, most of it has been fascinating and i have almost finished reading up on everything to this time,”

“Well as good as it is unfortunately there is at least one thing you won’t be able to read about though. It’s the tale of the greatest soldier to ever live, a stallion who sacrificed much for this land. A stallion who would later become my commanding officer after i was selected to join his unit. A stallion known by many soldiers around the world simple as, Big Boss,” Shining said and watched Celestia tense up as he spoke the name.

“Oh, that sounds like quite a tale. Why would it be left out if this ‘Big Boss was such a legendary soldier?” Luna said and everyone else watching nodded in agreement with her.

“Because he was branded a traitor, a terrorist, and public enemy number one,” Celestia decided to speak, she had hoped never to bring this up again, but unfortunately Shining had decided to for a reason she couldn’t yet figure out.

“Because you let him be branded!” Shining shouted surprising everyone and causing many to gasp.

“Shining Armor watch your tone!” Celestia stood tall flaring her wings. She seen many things in her long life but she had never expected to see Shining Armor react this way to something she said.

“I will not! Back then you called that a fair trial? It was anything but, the evidence presented was paper thin and you knew it! But yet you still believed the lies of those old idiots!” Shining stood his ground shouting back at the princess. “Hell following that farce of a trial you didn’t even bother to follow up on the so called ’evidence’. But luckily somepony did!” he said reaching into his bags and pulling out a folder and then slapping it out on the floor in front of Celestia. he watched as she looked wide eyed at some of the things the slid out slightly when the folder hit the ground. “it took me a long time to put the pieces together without causing any fuss. One wrong move and i could have been in the same situation and I couldn’t let Cadence, Twily, or my parents go through that. So i bided my time and waited, waited for the right time to ask question and gather intelligence, waited for those old corrupt idiots to retire along with their accomplices, i waited just like he taught me so that maybe one day i could stand here and tell you that you were lied to and because of it you made a mistake and an innocent stallion had his home turned against him,” he said panting a little from all the shouting. He watched as Celestia looked between him and the folder, she did that several times before turning around.

“Well if you’ve been keeping up like it looks like you have then i guess it doesn’t matter anymore then does it?” Everypony gasped when Princess Celestia spoke.

“Princess how could you say something like that!” Twilight said her voice as quiet as a whisper, shocked at the response from her lifelong teacher and mentor.

“Because as I and i assume your brother might know...The stallion known as Big Boss died nine years ago…” she said sounding sad. Twilight couldn’t see but if she could guess that her mentor might be crying slightly. “Nine years ago i knew of his whereabouts and silently kept track of that. One day i received a report that his base had been attacked by an unknown force and that his transport had been shot down with him inside. There were few survivors but...he died,” Celestia faced her throne thinking about the day she had received the report, she adjourned court early so no one would see the emotion on her face as she read every page.

“Oh yeah report number two two one five seven three six,” Clestia immediately spun in place a look of shock on her face as she heard Shining Armor recite the report number.

“How could you possibly…?” she said as it dawned on her. “You faked the report,” she watched as Shining nodded .

“Only one part of it, the attack did happen, and many soldier i knew died that day...but Big Boss didn’t die that day. His transport was hit and he was injured but he survived if only to go into a coma. And after that day I haven’t heard anything else,” he said looking to Applejack as did everyone else, she stared him up and down for what seemed like an eternity before she nodded, giving the signal that he was telling the truth.

“So what’s the point in telling us that!” Celestia said as her anger got the better of her. “what can somepony in a coma do for us especially if he’s been in one for nine years! He’s just as good as dead then!”

“But he’s not anymore,” Shingin said stopping Celestia in her tracks. “Otherwise i still wouldn’t have this. There’s an enchantment on it that would destroy if if the boss ever died or never woke up after a certain time. It’s also our way to get in touch with him and have him help us save Equestria,” Shining said as he rummaged around one of the bags for a second before he found what he was looking for and pulled out the guard badge for his old unit. A bright orange fox glared at all who stared at it while holding a knife in his mouth and above it in the same orange color in bold letters was the name.

FOXHOUND.

Author's Note

a new fic i came up with a couple of weeks ago after playing MGSV for awhile and then last night after the adderall took hold(yes i take adderall) i literally just sat down and belted this out in a couple of hours...it's much easier to do when you're not trying to write a ton of dialogue

Anyway i will say this i have not finished MGSV so i do not know the full ending but DO NOT SPOIL IT IN THE COMMENTS OR ANYTHING I WILL JUST INSTA DELETE YOU COMMENT YOU HAVE BEE WARNED!!!

I know that mgsV does have some graphic themes but i'm not sure how far i'm going to get into them so for now i'm keeping the story at teen...may update down the road whenever i get there

This isn't an exact copy of the story from MGSV but i will be taking parts of it. oh and as for the cover art it belongs to InkieHeart i had a link in the description...although i didn't ask...hope she doesn't get mad at me lowly fic writer.

Although i will say i don't know if i will let the art affect the story...it is an intriguing idea btu i'll thnk on ti whenever i get back to this

This has not been in editing though, my guys are somewhat busy atm and so instead of workign on my main story Their New Life In Equestria i decided to work on some side projects, this being the first of a possible couple. Please let me know what you think down below