Mass Effect: Shepard's Rebirth

by Redbow Rose

Rating: teen
Tags: Crossover, Main 6, My Little Pony: Friendship is Magic, Other
Length: 4714

Commander Shepard lives with a bloodstained past. All the choices he made leading up to the moment Death takes him for good. Or that's what the Commander thought.

Commander Shepard lives with a bloodstained past. All the choices he made leading up to the moment Death takes him for good.

At least that's what the Commander thought.

Finding himself in a land with all kinds of mythical creatures (mainly technicolor ponies), where war and violence have no place, he must choose to let go of the past be absorbed by Equestria's hidden darkness.
Little does he know that Fate kept him from Death for a reason.
A long vanquished enemy will return with a vengeance, shedding light on parts of history that were better left in the shadows.

Published 2014-08-17 08:50:05 UTC
Last updated 2016-01-12 21:02:03 UTC

Prologue

Prologue

“Have you decided?”

As the commander considered his options one thing was apparent... no matter what he did, Commander Shepard wasn’t getting out of this alive.

Commander Shepard stood in a previously undiscovered room, in front of him was the being that it housed... The Catalyst. All around the Citadel the Commander could see the destruction wrought by the still raging battle.The once awe-inspiring space station now buried under its own rubble. Outside, the cost of Commander Shepard’s desperate gamble could be seen. The remains of thousands of ships, with casualty counts reaching into the billions, was not unlike the debris field that once surrounded the Collector base. Cluttered, dead, and suicidal to traverse.Yet, despite all that, the Reaper threat was almost over.

Commander Shepard rallied the Galaxy’s forces for the largest confrontation the galaxy has ever seen, the battle for Earth. Shepard’s forces came en masse through the relays, massive, Element Zero powered constructs capable of sending a ship to the other side of the galaxy within minutes. Immediately after arriving the ships started hitting the Reapers with all they had, but the Reapers were prepared. Both sides sent fighters for initial combat. With Admiral Hackett leading the main force, Commander Shepard along with others involved in Operation:HAMMER, the force tasked with ensuring the success of the Crucible, flew down to Earth to assist the ground force led by Admiral Anderson.Unfortunately, Reaper forces were stronger than expected. By the time the Commander got to the forward operations base, less than 25% of HAMMER’s forces arrived.

Even with such small numbers, the Commander and what remained of HAMMER made one last push to the Beam, the only entrance into the Citadel. The Beam was a large matter transport used by Reaper forces to get human bodies onto the Citadel. If even one person made it to the Beam, then they would be able to open the arms of the Citadel. Doing so would allow Admiral Hackett to attach and arm the Crucible, a super weapon designed to end the Reaper threat once and for all. A super weapon originally thought to have been made by an extinct race, with only one survivor, known as the Protheans.

Everything was going as well as they dared hope, but before HAMMER could reach the Beam, Harbinger, the first Reaper ever created, attacked HAMMER, and with no cover in sight Harbinger decimated the force as they stormed the Beam quickly turning the bare clearing into a dead man’s land. The Normandy, Commander Shepard’s personal ship, was called in to evacuate those who were badly damaged. All those who stayed died.  All but two, Commander Shepard and Admiral Anderson. Suffering heavy wounds, they were able to reach the Beam.

While on the Citadel Shepard and Anderson were confronted by the Illusive Man,  the man who funded Project:Lazarus and brought Shepard back from the dead. The head of Cerberus, a pro-human organization with a habit of going too far, had become indoctrinated and infused with Reaper tech just as Saren had 3 years beforehand. Obsessed with the belief that he could control the Reaper he prevented Shepard and Anderson from opening the arms of the Citadel to connect and complete the Crucible. After the Commander helped the Illusive Man fight the Reaper influence the Illusive Man shot himself in the head, preventing the Reapers from regaining control and leaving the path clear for the Commander and Admiral to open the arms and allow Admiral Hackett to complete the Crucible.

As fate would have it moments after Anderson died and Shepard prepared to join him Admiral Hackett alerts him to the fact that the Crucible wasn’t firing. Shepard had to use the main console and fire it manually. Unfortunately the Commander had lost his strength due to to his wounds and found it failing him as he reached for the console, blacking out inches from his goal.

When he awoke, much to Shepard’s surprise, he found himself in an unexplored section of the Citadel. He could see Admiral Hackett’s forces still battling the Reapers outside, but losing steam. The room itself had only three things of notice. To his left the Commander saw what seemed to be an exposed power conduit, blue energy going through. To his right Shepard saw what seemed to be another power conduit, but closed and lighted by a red glow. Directly in front of him Shepard saw a beam of energised Element Zero, constant and illuminating.

“Hello there” Shepard turned to the source of the voice and saw the hologram of a child. A child that’s been haunting the Commander ever since he fled Earth. Ignoring the disturbing, ghost-like image the Commander asked the hologram “who are you?”

“I am the Catalyst.”

“I thought the Citadel was the Catalyst.”

“The Citadel is my body. I am it’s mind. Now, you have come here hoping to stop the Reapers. Correct?”

“I have.”

“Well then, before you do so I ask you to listen to the truth behind the Reapers. They are not the evil you think they are.”“I’ve seen little to convince me otherwise.” Shepard replied.

“A choice?”

“A choice that will determine the fate of the galaxy. As I’m sure you’ve noticed that there are three point of interest in this room. They are your choices. If you still wish to destroy the Reapers then destroy the power conduit. Doing so will overload the Crucible and in turn annihilate the Reapers, but be warned. This will destroy all synthetic life, such as the Geth. Remember that this will most likely destroy you to, as you are also partially synthetic. If you believe that you can lead the galaxy into a brighter future then grab the pylons. Your body will be destroyed, but your mind will be downloaded into the Reaper network as the main AI. If you wish to promote harmony between synthetics and organics by eliminating the distinction between the two then dive into the beam of Element Zero. You body and mind will be lost, but organics and synthetics will become equals.”

“What if I don’t choose those options?” The Commander asked.

The Catalyst looked at him and said, without any change in tone, ”The cycle will continue, And you will die. You have five minutes to make a choice. After that you will lose the strength to live.” Even as he said it Shepard could rapidly feel his life force draining away. He had to make a decision, and soon. He couldn’t destroy synthetic life, the Geth had just gained individuality and were giving their best to save the galaxy that hated them. He didn’t trust himself with the control of all Reapers. He feared that his mind might collapse after the experience was over. If he didn’t choose anything then the war was lost. That left only one option.

“Have you decided?” The catalyst asked.

“Yes, I have.”

“Then go.”Commander Shepard looked ahead at the glowing beam of Element Zero and, taking a deep breath, slowly started to run.

********

“So, why are we here again?” asked Rainbow Dash for what, to Twilight at least, seemed to be the hundredth time. “I told you, Rainbow, I’m going to conduct an experiment with an artifact that pre-dates even the Discordian Era. Because of the nature of the experiment and the age of the artifact I assumed you girls would like to watch. If this works it could be one of the most important discoveries in Equestrian history, possibly even more important than Starswirl the Bearded’s work on-”

“Yeah that’s cool and all, but I still want to know why you thought I would like it.”

“I knew you liked ancient artifacts so I honestly thought you would be the most excited.”

“I like artifacts Daring Do retrieved herself. This wasn’t taken from an ancient temple or something by her, so I see nothing awesome about it.”

“Well, Rainbow, did you know-”

“I’m so sorry for interrupting, darling, but I would prefer to see what this artifact does. The suspense you’ve built up is absolutely dreadful.”Interrupted Rarity, stopping Twilight Sparkle and Rainbow Dash from having yet another debate.”Yeah! Come on, Twilight, show us what it does!”

“Okay”. Darn Rainbow Dash, she really needs to appreciate history more. The girls are right, though. I’ve done my best to get them excited about it so the suspense is probably killing them. Besides, if this works it’ll show Rainbow that an artifact doesn’t have to come out of a Daring Do adventure to be interesting.

Twilight Sparkle had been given a very special task after Discord’s reformation by Princess Celestia herself. “Twilight, I have a very important favor to ask of you” Twilight was standing outside the Golden Oaks Library when the princess came up to her.”Anything for you, Princess Celestia!”

“It’s nice to see you’re chipper after todays events, Twilight.” Princess Celestia said with a warm smile.”In any case I think you’ll like this one. A few days ago Princess Luna mentioned to me that a very important artifact was found intact at our old castle. I need you to go to the castle and complete the research on it.”

“Research?”

“Yes, unfortunately the artifact was left behind during the...Nightmare incident.” Princess Celestia gave a small frown as she recalled what happened years beforehoof, but it quickly disappeared as she continued on.“Many bright minds have poured their heart and soul into this research, including Starswirl the bearded.” The princess flashed Twilight a knowing smile as she tried, and failed, to keep herself from fillyfaning over the thought of completing research Starswirl himself worked on. “Now I know you’ll want to start on this right away”, continued Princess Celestia,”but remember to be careful when traveling to the old castle, eat, sleep, and other necessary things, Twilight.”

“D-Don’t worry princess, I promise I’ll take care of myself.” Said Twilight, blushing from the princess’s jab at her old study habits.

That had been a week ago. Fortunately the preservation spells on the old research scrolls were still intact. The notes themselves were also nearly to a testable level. After a week of intense work (all the while heeding the princess’s advice) Twilight was ready to experiment with the artifact. After getting her best friends together Twilight brought them all to the old castle.

“Everything's ready for you now, Twilight!” Said Spike, having just done a check on Twilight’s materials. “Thank you, Spike,”Twilight said before levitating over a rock.”Now, girls, are you ready to see history in the making?”Twilight asked cheerfully.

“Not to be rude, Twi, but ah would like tah see what yer makin’ such a fuss about.” Apple Jack said. “Fine,” giving her friend AJ a small frown Twilight levitated the small rock into the middle and held it there. Before Rainbow could start complaining about nothing happening the rock, which before had been black, was now a glowing blue. A few moments later, with a large CRACK, the rock broke apart and left behind a glowing blue aura (growing more purple by the second) that soon seeped into the artifact. Twilight and the others watched, awestruck, as the ancient gyros started turning and purple cracks appeared on the artifact’s ancient coating of dirt and grime to reveal the elegant machine beneath.

“My goodness, Twilight, I must say that this artifact looks quite beautiful without all that dirt!” Said an awestruck Rarity. “Yes, Twilight, it’s very pretty.”Fluttershy quietly commented. “Well, it looks cool,” said Rainbow Dash, recovering from her surprise,”but what does it do?”

“This time I’ll just show you.”Said a smirking Twilight.”Apple Jack, may I borrow a bit please?”

“Uh, sure, Twi.” Said a confused Apple Jack as she hoofed over a bit.”Thank you, Apple Jack. Now watch the bit closely.” If my calculations are correct this bit will shot far past the moon. The ponies and dragon watched the bit get closer and closer to the artifact. A bolt of energy suddenly grabbed the bit, and before anypony could react, the bit was shot off towards the night sky.

“What just happened?” Asked a stunned Rainbow.

“You see, Rainbow, the artifact used the rock’s energy that I boosted to condense and accelerate the bit’s mass. Right now the bit is far past our solar system. The spell I put on it will bring the bit back for us to examine in a few minutes.”

“Why does it do that?” Pinkie Pie asked.

“Well, I think it’s actually a prototype space travel device.”Pinkie suddenly gasped.

“Does that mean that there are ALIENS! Oh my gosh I can’t believe it, real aliens! Are they ponies too? What if they walk on two legs, have things called hands, and watch a show that’s all about us?! That would be sooo cool, and weird. I mean what if they saw me get all sad that one time and made a scary fanfic with a sad me, Rainbow Dash, and CUPCAKES!? I wouldn’t like that at all because I would never bake Rainbow into a cupcake, I mean-”

“PINKIE! For the love of Celestia please stop!”

“Okie Dokie Lokie, Rainbow!”

“Umm, Twilight?”

“Ugh. Yes, Fluttershy?”Twilight replied while trying to stop the oncoming headache.

“Is the artifact supposed to be going that fast?”

“What do you mean?”

As Twilight looked at the artifact and saw what had caught Fluttershy’s eye. The artifact gyros, which were going at a slow pace beforehoof, were now moving at a considerably faster rate, and were visibly getting faster and more unstable.”Uh, Twilight? Ah don’t think that’s ‘spose tah happen” Apple Jack had also caught on and gave her friend a worried look. Seeing the overload signs Twilight knew only one thing to do.

“Everypony, get by me, now!” Seeing the danger Rainbow Dash, Pinkie Pie, Rarity, and Spike rushed to Twilight, Fluttershy, and Apple Jack as Twilight created a barrier over them all. Right after the artifact exploded and an object crashed down through the open roof of the castle filling the air with dust.

********

Every step was an agony worse than hell. Any lesser man would have been driven insane from the pain. Any lesser man would have died the moment he sustained such wounds. Despite this the Commander went on, his goal growing ever so closer. With every step he remembered who had died for this moment.Kaiden, Thane, Morden, Anderson.

Tali

The true face of the woman he loved flashed through his mind. He promised her that he would live. He promised her that they would build a house on Rannoch. I’m sorry, Tali, but I won’t be coming home after this. As the Commander took one last leaping step one more thought presented itself to him. Garrus. Please take care of Tali and everyone. Don’t let Joker try to save me. Please...live.

Shepard dove into the beam of Element Zero and stopped feeling pain. His DNA was being absorbed. His body, a balance between synthetic and organic, was a perfect example for the Crucible to replicate. He would die, yes, but others would li-

Shepard felt a dull thunk on his backside. A millisecond later the Commander felt his nerves come back to life as his body was racked in mind shattering pain. His body twisted and convulsed, as if trying to recreate itself but forgot how it was supposed to look. Shepard's existence was only pain for what seemed like eternity, the Element Zero trying to gain the needed DNA by dissolving him, while his body fought back by recreating itself, as if by magic. Eventually It seemed that the Element Zero got all it needed, as Shepard fell from the beam’s hold and was pulled by whatever had hit him in the first place.

Suddenly, when the Crucible fired the Commander could feel himself being shot towards an unknown location at Mass Relay speed. He was barely aware of the field that kicked in when he reached his destination, or the crash that followed.

********

Shepard regained consciousness soon after the crash. His body, sore and exhausted, barely had enough strength to get him up on his hands and knees, let alone up on his feet. Looking around he could only see dust, but he could hear coughing. That meant that others had gotten caught up in the crash.

“H-Hello?” Hearing the voice the Commander tried to locate the owner, but to no avail. His senses weren’t working properly. “M-My name is Tw-Twilight Sparkle. Wh-What’s your name?” Sounds feminine… and nervous...no surprise… I just crashed through the roof…I probably look like hell…”My name is…Commander Shepard…” Damn… I won’t be able… to stay conscious…for much longer…”A-Are you okay?” The voice asked. Finally able to pinpoint the location of the speaker, the Commander looked forward past the raised dust to see

...a purple unicorn? Unable to stay conscious for any longer the Commander collapsed on the floor.

Chapter 1: The Alien

Twilight Sparkle didn’t know what to do. Her experiment has been going perfectly, but within a few seconds it had gone horribly wrong. Her calculations were perfect, every variable had been accounted for, it all pointed to the experiment going perfectly. What had gone wrong? What was the unknown factor?

Thankfully she was  able to create a barrier around them before the artifact exploded, leaving them coughing and shaken, but otherwise unharmed. Before Twilight could investigate the remains of the artifact she heard movement from the test area. She froze, along with everypony else, fearing what it could be.

They all watched in horror as a silhouette of...something... rose from the remains of the ancient device. After what felt like an eternity, the dust cleared enough to see that the being in front of them had the shape of a pony. She let out a breath she hadn’t known she was holding in, though she was still wary of the new and explosive arrival.

“H-hello, m-my n-name is Twi-Twilight Sparkle. W-what’s yours?” The librarian asked, trying to be friendly but failing to keep the fear she still had out of her voice.”My name is...Commander Shepard.”

“A-are you o-okay?” Twilight asked the pony, hearing the strain in his voice as he struggled to say that one sentence. In response the pony looked at Twilight before falling to the ground, unconscious.

“Oooh, so THAT was the doozy!” After taking a few minutes to process what Pinkie had just said, Twilight then facehoofed, recalling what had happened on the way to the old castle.

Twilight and the girls had been walking through the Everfree Forest, taking care to stay on the path. Rainbow Dash had been arguing with her about the artifact when Pinkie started shaking violently. “WwOoOoAaAaHhHh!” Everypony froze and watched as Pinkie continued shaking, knowing what Pinkie Pie’s Pinkie Sense meant. “Wow! There’s gonna be one HECK of a doozy at the old castle!” Pinkie said cheerfully.

Twilight quickly recovered, seeing this as a proving point in her argument. “See? Even Pinkie’s Pinkie Sense shows that the artifact will be amazing!” Applejack then decided to intrude on the argument. “Twilight, sorry to burst yer bubble, but that’s not how Pinkie’s Pinkie Sense works. If she’s sayin’ it’ll be a doozy then nopony, and ah do mean nopony, will know what will happen. Last time you tried to figure out how it worked, ya got injured  and we got chased by an angry hydra!”

Twilight shivered, the memory all too clear for her. She had worn an umbrella on her head for weeks after the incident. She hated how Pinkie seemed to disregard the laws of reality at times. She gave Discord a run for his bits. “Even so,” Twilight said, “I still have a firm belief that everything holds to some set of rules, even if it doesn’t follow the...conventional ones. So, I believe that Pinkie’s Pinkie Sense acts in relation to Pinkie herself. If something will fall, Pinkie will only react if it will affect her. After all, I don’t see her Pinkie Sense acting up all the time! So, because Pinkie has no idea what the Artifact will do, her Pinkie Sense will tell her it’s a doozy. Because I DO know what it will do, it isn’t a doozy for me. So, Pinkie’s Pinkie Sense will only be in relation to her.”

Applejack gave Twilight a flat look and raised an eyebrow. “Fine, believe what ya will, but I bet ya ten bits that yer wrong.” Twilight, confident that she had finally found a rule that even Pinkie had to abide by, happily agreed. “You’re on!” She said.

Twilight sighed, seeing logic fail to hold the conundrum that was Pinkie Pie once more. “O-oh my! Is he ok-kay?” Fluttershy coughed out, now more concerned than scared. “W-well,” Rarity said as she tried to get out of the dust-polluted air, “it doesn’t look that way. I think we should ALL get out of this horrid dust, and it just can’t be any good for our new friend here.” After everypony coughed their agreement, they all went upstairs to the old castle’s throne room with Applejack and Rainbow Dash carrying the surprisingly heavy stallion between them.

“Mother of Celestia, he’s heavy!” Rainbow complained. “Ah hear ya. This feller is heavier than Big Macintosh.” The farm pony agreed. After putting down the mystery pony, Rainbow and AJ joined their friends in recovering from the excitement. After a while Pinkie decided to start a conversation. “So, what are we gonna do with the alien?”

Twilight blinked. “Alien? What alien?”

“Oh you know, the alien Rainbow and Applejack carried up here! I mean, he has to be an alien because he came from outer space instead of the bit!” Pinkie Pie then gasped. “What if when we launched the bit it hit him, and when you started pulling the bit back it pulled him too! What if while the bit was pulling him it turned him INTO a pony! That’s amazing! This way I can throw him a ‘Welcome to Equestria’ party, a ‘Welcome to Ponyville’ party, and a ‘Have fun being a pony’ party! That’s THREE parties at once! It’ll be the best. Triparty. EVER!” Pinkie then finished her thought by pulling out her party cannon and shooting out confetti.

Twilight and the others, of course, had to take a bit of time processing what Pinkie said. When they had finally understood what the party pony had gone on about they all took a closer look at the unconscious pony, trying to find anything out of the ordinary with him. He looked like a normal earth pony. He had a light brown coat, and a black mane and tail. Twilight opened his eyes and just saw blue, regular eyes. Nothing abnormal there. He was muscular, and Applejack said that he was probably a hard worker. He was covered in a burnt material though, and Twilight ripped a piece off to research later.

“He doesn’t look like an alien to me.” Rainbow Dash said, frowning. “The only weird thing about him is his outfit and how heavy he is.” Twilight thought for a moment. “Well, we can try to piece together who he is by what we know. His name is Commander Shepard, he has a hard worker’s build, and is wearing the charred remains of something. He is obviously an alien soldier, and a leader if the title ‘Commander’ is anything to go by. He is probably wearing the remains of his armor, though it’s not like anything I’ve seen. It’s also baffling that, despite his armor’s condition, he is virtually unharmed. Perhaps Pinkie is right...somehow...and the bit hit him and caused a reaction with his body. We need to take him to ponyville and help him recover, we can learn more there.” Twilight finished, the logical thinking helping her calm down.

“Well, you can just teleport us to Ponyville, right? It’ll take forever if we have to drag his heavy flank there!” Rainbow pointed out. Twilight, to RD’s dismay, shook her head. “I can’t do that for multiple reasons. One, Ponyville is too far away, so at best I’d make it to Fluttershy’s cottage. Two, That’s just on my own. Including all of us, I’d not make it too far. Finally, I really doubt that it’s a good idea to teleport an alien who could react badly to the process. As much as I know that it’ll be hard to carry him, we don’t have a choice unless he wakes up and walks on his own.” Rainbow just groaned and slumped to the floor.

“Ah don’t see what the problem is.” The cowpony said. Rainbow gave her a blank stare. “Well, if we work smart, and not hard then movin’ him won’t be a problem. I’ve had to haul mah brother to the farm from the bar after one too many drinks. Besides, Rainbow, think of it as Wonderbolts trainin’!” The prismatic pegasus just grumbled and crossed her hooves.

“Well...I think I can help with moving him.” Fluttershy said. “That is, if you don’t mind…”

“How  so, Fluttershy?” Twilight asked. “Well,” Fluttershy started, “when you move someone that’s unconscious, it helps to give them a massage. After all, when he wakes up he’d be easier to talk to when he is calm and rested.” Twilight thought for a moment. “Well we definitely want him to be calm and relaxed when he wakes up...okay Fluttershy, it sounds good to me!” The unicorn finished with a smile.

The yellow pegasus nodded and trotted over to the unconscious stallion and started to gently rub his back in circles with her hooves. She frowned as she discovered how tense his back was. “You’ve been through a lot of stress through recently, haven’t you?...” She said quietly. She continued to massage the stallion, wondering what happened to him to put him in such a sorry state. As went on, she also looked at the armor he was wearing, and found something faint upon it. “Um...Twilight? What does N7 mean?” The butter colored mare asked.

Twilight frowned and looked where Fluttershy was pointing and saw the letter and number, barely visible. “I don’t know Fluttershy, but it looks like it means something important. We’ll have to ask him when he wakes up.” Rainbow Dash, who had been relaxing, took interest at this point. “Hey, maybe it means that he is part of a special group? After all, I bet that his military has too many soldiers to give them numbers like that. What if we came across one of their best, a soldier who was willing to throw his life away to save everyone when BAM! Your experiment accidentally saves him! Oooh that be so AWESOME!”

“Well, Rainbow, if that’s the case then we better get him to ponyville safely.” Twilight said. “Fluttershy, I want you to head to Ponyville with Pinkie and Rarity and tell the hospital to expect a special guest, and give him a room of his own. Dash, AJ, Spike, and myself will salvage what we can and bring back the Commander. That okay with everypony?”

Rarity frowned. “Yes, Twilight, I’m sure nopony would mind the arrangements, but now that you’ve mentioned him...where IS Spike? I haven’t seen him for a quite a while.” Twilight rolled her eyes. “He’s probably down by the treasury. He says he found a lot of gems around there and likes to try picking the lock on the treasury door. I keep telling him that those gems belong to the princesses, but he insists that ruins are ‘fair game’. I’ll go get him.” As Twilight started towards the stairs, she and the others froze after hearing a loud roar. “What in tarnation was that?!” Applejack exclaimed. “Trouble. Let's hurry!” Twilight said, before running down the stairs, the others following soon after.

Just after the mares left, the mystery stallion groaned. Slowly he got up, rubbing his head with a hoof. “Son of a...where am I?” He look around a bit before realizing something very different about himself. “Well...that’s different. At least I know I’m not dead, though.” Hearing commotion from the nearby staircase the stallion shakily got up. “What better way to see if I’m at 100% than to beat the crap out of things till I feel better.” Shaking his head, he started down the stairs.