Close Quarters

Summary – John Shepard was tired. Almost 4 years spent fighting the reapers and for what? 3 crappy choices, each worse than the last. At the end of the war, in that final moment, he's had enough. All he wanted was lost back on Virmire. Kaidan told him to save Ashley, and he did, but at the cost of his own happiness. So, deciding he's had enough of bending to the whims of a computer generated image, he crosses a few wires and ends up back on Virmire with a second chance. A chance to end the war before it starts, a chance to live.

[Not a story of Shepard going back in time and kicking the Reapers asses with his future knowledge. This is going to focus more on Shepard getting back what he had lost, with him lending the other Shepard an occasional helping hand.]

Disclaimer: I do not own Mass Effect. If I did, the ending would be better, and Shepard would get to punch Illusive Man in the face.

Pairings;

John Shepard [Paragade/Sole Survivor/Ruthless/Colonist/Vanguard]/Kaidan Alenko

James Shepard [Paragon/War Hero/Spacer/Soldier]/Miranda Lawson

CHAPTER 1: A CHOICE

"The paths are open. You must choose" John Shepard, Commander of the Normandy and First Human Spectre stood in disbelief as a computer representation of his recurring nightmare told him to choose between genocide, control, or fundamentally changing everyone's DNA. After everything he had fought for, everyone who had been sacrificed to make it this far, there was no end. The aftershocks of his choice would be felt all across the galaxy. The mass relays would be destroyed, stranding all the fleets in the Sol System, slowly killing by mass starvation. If he chose the control pillar he would end up no better than the reapers, losing what kept him in check, his humanity. Synergy sounded like the best option, until you factored in that no man can decide such a choice for anyone but himself.

As he thought about his options, a memory welled up of another impossible choice. Ashley or Kaidan. His duty said Ashley, his heart said Kaidan. Logically it made sense to protect the bomb, it being the only way to destroy the cloning facility. But in following the logical decision, he left Kaidan to die alone on Virmire, the tattered remnants of his heart with him. Familiar feelings of guilt, pain, longing rose in him, and he swore to never make that choice again.

John stood on the pathway in his burned and melted armor, clutching his abdomen in an effort to stop the bleeding, and made a different choice. Turning towards the ghostly image of the catalyst he limped to the lone computer console, releasing his pistol so he could input commands.

The beeping of the console was interrupted by a child's voice, "What are you doing? You must choose, or everything will be lost."

"I am choosing. Just wired a little differently." His worn voice answered. He was so tired…

"What do you mean? There are no other choices." A guttural laugh rang out as John finished inputting the last few commands.

"I didn't make a new choice, I choose all three. I figure it's better than any individual one, and personally, I don't give a flying fuck what you say. I've fought too hard and lost too much to let the end of the war be dictated by a figment of my imagination." So saying he closed the console and input a command into his barely functioning omnitool.

The catalyst looked behind at the whirring machinery, confused as to what the human had done. It examined the console within its mind, tracing the wires and input commands. It whirled in shock, yelling after the retreating human.

"What did you do? The Citadel is not meant to utilize that much power. It will destroy itself before it fires! Shepard!"

It was ignored, along with its ranting's. John limped back over to the elevator and descended until he was in the remains of the citadel embassy. Sparks were emitting from blown transformers and lights were flickering ominously as the citadel gathered power at its core.

With a ding the elevator doors opened and John grasped the edge to steady himself before continuing onward to his destination: spectre headquarters.

"Spectre status recognized. Welcome, Commander Shepard" the doors whirred open and John limped as fast as his broken body could to the personnel lockers. Inputting his own code he opened the locker to reveal a set of his custom Ariake/Hahne-Kedar armor along with much needed medical supplies.

With a hiss, he started to peel off as much of his burned armor as he could, applying medi-gel to each uncovered wound. When his torso was fully bare he dug two of his fingers and retrieved the mass-accelerator round in his lower abdomen, and then applied as much gel as he safely could before tightly wrapping the entirety of his abdomen in bandages. Feeling the pain retreat down to a dull roar he proceeded to put on the new armor, feeling more himself with each piece added.

Done with the body armor he grasped the last piece, a recon hood. He figured it would protect his ravaged face from even more damage. Now suited up he walked to the armory, taking note of the now almost ear-splitting whine emitting from the citadel. Being a Vanguard he could only carry so much weight in weapons. From the somewhat limited selection, as none of the lower tier weapons were available, he chose an M77 Palladin and an M99 Saber. A mild debate with himself and he also picked up a Black Widow rifle. Now suitably geared up and feeling secure in the knowledge that he could take on whatever the universe threw at him next, he left and went back the way he came.

At this point the citadel was practically vibrating underfoot and the undulations of the floor were starting to affect the surroundings. John was looking for survivors, if any were left, and bookshelves' crashing to the floor was not helping.

"Hello? Is there anyone left alive? Can anyone hear me?" Nothing but the whine of the Citadel reached his ears and he let out a grunt of frustration. As John turned back towards the center of the Citadel a particularly harsh shake propelled him off of his feet.

Adrenaline spiking once more he shoved himself to his feet and began to run back to the center of the Citadel where, years before, he and his team had taken the relay from Ilos to the Citadel. Sprinting through the debris and steadying himself whenever the floor moved, John was distracted by his sputtering ear-piece.

"…ander…Comma…epard, can you…ear me?" Still running he raised his hand to his ear and simultaneously checked his omni-tool to try and clear up the frequency.

"Commander Shepard, are you there? The crucible isn't firing, and we've lost contact with Anderson." Recognizing Admiral Hackett on the comm., John responded, "Sir, the Citadel is powering up, I'm on my way to the control console to check its status. I don't know what will happen, I think it best that the remains of the fleets retreat…including the Normandy."

There was silence on the line for several seconds, in which the Citadel gave a jarring shudder and John stumbled and fell to his knees, before, "Understood Commander. And Shepard? Well done." The transmission cut and John was on his own.

Giving a slight shake of his head he continued his run to the main console. However, he would never make it. Still on the Presidium level the Citadel gave a giant jolt to the side, sending John crashing into the remains of the miniature relay. He stumbled to his feet, now frantic, and almost missed the humming of the supposedly inactive relay. It seems, that whatever wires he crossed on that original console somehow reactivated the relay.

He had stayed too long. An ear-splitting scream came from the Citadel, with the relay resonating with it, and the center of the relay exploded with energy. John, practically on top of it, was mass-accelerated along with the energy beam from the rest of the Citadel.

The fleet, which had retreated a safe distance away from the Citadel, witnessed a bright flash of light followed by a beam of energy that impacted the relay and seemed to energize the relay until it too emitted a beam of energy. The Reapers were vaporized, not even atoms remaining, their consciousness's, and indoctrination, dying with them.

Admiral Steven Hackett stood on the command deck watching, and gave a silent salute to the man who made it possible for them to win. A man whose consciousness was quickly fading as he was flung across the galaxy, until with a last thought he faded.

"Kaidan…"

It was bright. This was Johns' first thought as sunlight filtered through the trees and hit his closed eyelids. John tried opening his eyes, which took a few moments as they adjusted, and sat up with a groan. Taking in his surroundings he swore he had been here before. He rolled over onto his hands and knees and levered himself up until he was standing and began to look around. This semi-peaceful moment was interrupted with the sharp crack of gunfire. Johns' head whipped around, almost giving him a crick in his neck, and ran towards the sounds of the fire fight.

As he ran he continued to have that feeling, as though he should remember what was going on and where he was. It wasn't until he heard the familiar sounds of geth communicating with one another and salarian commands interspersed with a rare human voice that he remembered.

Virmire. The planet of his nightmares. John stopped almost instantly, his mind flashing back to all those years ago and that terrible choice. But how did he get here? Virmire was practically a radioactive wasteland after the nuke went off, it definitely didn't have any trees or rushing water on it anymore. An alarm went off in the back of his mind, and without being fully conscious of what he was doing he typed a frequency into his omni-tool and hit enter.

The sound of chatter filled his ear, one voice driving itself into his heart.

"Shepard, the bomb is more important. Leave me, get Ashley. I'll hold out." John couldn't breathe. This wasn't possible. And then a somewhat bigger shock, but one not as impactful, he heard his own voice over the comm. unit.

"Kaidan…Understood Major, I'll get Ashley." Not willing to let his biggest regret play out exactly the same, John interrupted the communication.

"I'll retrieve the Major, and meet you at your ship." All communication stopped, the sounds of gunfire all that remained, until, "Who is this? Identify."

Thinking quickly, John said, "I'm a Spectre. Major, what's your location?"

Clearly hesitant to tell the stranger, with the other Shepard saying that there wasn't enough time, Kaidan relayed his coordinates. Bringing up a mental map of himself and where Kaidan was, he gathered his biotics and charged to Kaidan.

For the Major, one second he's telling the supposed Spectre where he is and the next he sees a black and red armored individual appear in a flash of blue. Not sure what had happened he continued to fire at the geth. Kaidan watched as the man glowed blue in what could only be biotics before he arched and drove his fist into the ground, a pulse detonating around him and sending geth units flying. The man stood up and before any of the geth could recover he sent shockwaves and warps at the geth like it was a free-for-all, before grabbing one of the closer geth and sending a biotically driven punch straight into its chest cavity. The armored geth crumpled like tissue paper around the man's arm, and he used the body to smash another geth before sending the body back at a group of them. At this point Kaidan had stopped firing as he was in too much shock at the one man army tearing up the geth troops like they weren't even there.

John released another Nova and followed it with a charge at the geth Prime he saw. Biotics glowing brightly he brought his arm back and released his omni-blade, bringing it up and impaling it right through the Prime's head. The body teetered a little before crashing to the ground. John remained kneeling for a moment, checking for any more geth before retracting the blade and rising. With the fight over he slowly turned, looking at the man whose death had haunted him for the last 4 years. When he saw Kaidan he nearly wanted to cry. Kaidan was just as he remembered, a soldier to the core.

Kaidan kept his gun up, slightly lowered but in a position that allowed him easy aim, as the biotic powerhouse stood from the Prime he had just stabbed. The man was wearing the most hi-tech armor Kaidan had ever seen, a blend of dark crimson and matte black, and had a hood of some sort covering his face. Kaidan started forwards, continuously scanning his surroundings as he made his way towards the man.

"You're a Spectre?"

"Correct." Kaidan eyed him suspiciously for a second.

"The only human Spectre is Commander Shepard. You're lying." To emphasize his point he raised his rifle a bit.

"Right and Wrong. We can debate this later; right now we have to get to the ship before it leaves." As if to hammer this home the other Shepard's voice came over the comm.

"Kaidan, I have Ash. Where are you?" Kaidan opened his mouth to respond but let out a muffled curse instead as John grabbed him and swung him over his shoulder in a fireman's carry.

"What the hell-" he was cut off as John gathered his biotics and charged to where he remembered the ship being.

John levered Kaidan off his shoulder and pushed him in front as they arrived in the middle of the firefight between the other Shepard and Saren. Not letting Kaidan get a word in edgewise John propelled him onto the Normandy. John swung him around to face him and yelled, "Stay here!" before turning and once again charging, this time at his alternate self.

The other Shepard was being strangled by Saren a couple feet above the ground. He raised his fist to punch the Turian in the face when a bright flash of blue light momentarily blinded him. When he could see again he saw an armored man throw Saren into the wall, it cracking with the force of the biotically enhanced throw. Saren crumpled to the ground and John spun around to the other Shepard.

"We need to leave. Get to the Normandy." He nodded, grasping his throat slightly, and ran back to the Normandy. John watched for a moment before striding over to Saren and wrapping his hand around his throat. Bringing the Turian face-to-face he said, "Tell Sovereign he will lose, and to pass the message onto Harbinger for me, ok? The Reapers will never win." Saren struggled for a second before gasping out, "Who are you to speak to me?"

A mirthless smirk formed on Johns' face, his mask hiding it. "I am what the Reapers fear. No more, no less." Dropping Saren John turned and ran for the Normandy, giving a biotically charged leap to land on the rising ramp.

John slowly walked up the ramp as the ship rose and left Virmire, his thoughts finally catching up with him. He had saved Kaidan, both he and Ashley had made it off of Virmire alive. And there was another Shepard. His alternate self seemed different, and in more than just the physical sense. It was how he carried himself, at least the little John had seen. Less weight on his shoulders, less grief weighing him down. If events were to play out like he remembered them, John could not make any overt changes until Sovereign was destroyed. After that, there was a two year gap before he had destroyed the collector base and then 6 months after that was when the Reapers showed up. He had to play this out right, or billions of people would die, just like before. He couldn't tell anyone who he was, Shepard was the only one who could unite the galaxy, and John didn't have the prerequisites in this place. No one knew who he was, and hopefully it was going to stay that way. Though he didn't know how he was going to pull that off…

He was startled out of his thoughts by the very object of his contemplation. The other Shepard stood, arms crossed, in front of the elevator.

"You need to come with me to the debriefing room." John gave a nod to show his assent, and followed his alternate self.

They stood silently in the elevator, and exited together on the bridge. Down the stairs and into the circular room where the entire crew was seated. John stood near the entrance, not sure where to sit, as the other Shepard stood in the center.

"Ok, the mission was a success. Saren's cloning facility was destroyed, and everyone made it off. Speaking of which," he turned to John, "Not that I'm not grateful for your assistance, but who are you? And how did you get there? You are human, at least in shape, and I'm the only human Spectre, so the truth would be nice." The other Shepard was squared up, arms crossed and stance that of someone who knows he's right.

John spoke, the masks vocal piece scrambling his voice into something semi-robotic. "I did not lie, I am a Spectre, and have the authorization codes to prove it. The rest is classified."

The other Shepard waited a second, probably for a name. With none forthcoming he said, "How about a name, then?"

John considered the man before him. "What is your name?" The other Shepard looked almost startled for a moment, as if he couldn't understand how someone wouldn't know who the first human spectre was.

"James Shepard, First Human Spectre and Commander of the SSV Normandy. Now answer my questions. I won't ask again."

John looked around the room, taking in the various expressions of the crew. Ashley looked like the consummate soldier, hard faced and supporting her Commander. Garrus and Wrex looked almost bored, as if they couldn't care less about the confrontation, though Garrus' mandibles were twitching anxiously. Liara looked slightly nervous in the face of the confrontation, and Kaidan…Kaidan was the hardest to read. His face was inscrutable as he looked between John and James.

Looking back at James John let out a weary sigh. He was just so tired…

John opened his mouth to speak only to feel the ship swaying sideways. That's odd, he thought, as the ship continued to move. Joker's usually better than this. His thoughts were cut off by the edges of his vision fading in and out. It was then that John understood what was happening, and with his last conscious thought, programmed his mask to be irremovable. So tired… his last memory was of the floor rushing up to meet him before his vision went black.

A/N - So, a reviewer from a different story of mine wanted me to continue it, but it was a one-shot and I couldn't really formulate a plot for what happened after, so this story was born. It's a little different, and I'm not sure yet where I'm going to take it, so let me know what you think.