While many of my fellow authors take time to rewrite the ending to Mass Effect 3, or suppose it was all a dream, having played through ME3 four different times now, taking time to do every side quest and study every choice in the game, I think I've come to be pretty satisfied with how the ending of the game goes, with some obvious plot holes and/or points that weren't really thought important.
My story picks up at the end of the Mass Effect 3 game, assuming a Paragon player and 5k+ war assets. This is more about the aftermath than anything else, so I'll try to make it interesting. I welcome any and all comments and feedback.
Also, though I played with my own custom name and all, I'll substitute the generic for ease of reference, though my character will be most decidedly Male.
Update 2: This is a rewrite of the story to better fit with the extended cut ending, and to polish up my own so-so writing, I hope. Again, your feedback is greatly appreciated.
Even before he could open his eyes, John felt the burn of the acrid stench of ozone and burning materials, their overwhelming foul odors stifling his breaths and sending him into spasms of coughs. With every breath he fought to take in enough clean air to ward off the growing throb of his body, though it refused to move at his command. Several bones were broken, judging by the pain that shot through him every time he attempted a movement, and the burning in his stomach reminded him that the hole there was real, and not simply a dream.
A sense of fear and dread washed over him as he tried to relax, trying to place where he was. He remembered earth, remembered rushing forward towards the beam, but after that, his mind grew hazy and the memories only came with washes of pain and nausea that discouraged him from thinking on it too hard. Where am I? What is this place?
Beneath his body and torn armor, he felt the sharp edges and jabs of broken plasteel and ceramic materials, and the weight crossing his numb legs told him he was pinned by something. His whole body felt cold, and as his body shivered, growing cold, the pain sparked through him like bolts of electricity from a live wire.
With a groan, he tried again to move, to turn his head, to do something. With relief, he managed to opened his eyes, but immediately wished he hadn't for the wave of nausea and sharp stab of pain that invaded his mind. From somewhere behind him, he thought he heard the sound of metal beams collapsing, and the curses of some being. An Enemy? God, I'm trapped here and someone's coming. "Commander, are you in here? Anyone alive in here?"
The male voice bellowing into the chamber was not altered and synthetic like those he'd heard from the Cerberus shock troopers. And it sounded human. Wherever he was, at least there were humans here, too. The creak and groan of more debris shifting under weight could be heard, along with the shuddering shriek of metal moving in ways it wasn't very happy to go.
John';s eyes darted around, fixing on various points. He could see beyond his head a blackened bulkhead, and part of a large open starscape, debris floating serenely as though drifting in a timeless ocean. He recognized the large petal-like pieces floating so close. The Citadel! That was it, he was on the Citadel! But why had he been there? His vision filled with the sealed breathing mask of standard Marine armor, the sounds of the man's air processing system hissing and blowing jets of warmth into his face. The grey eyes behind the mask studied him before taking a light and moving it before his eyes.
The shock of light pained him, set his head on fire as though someone had hit him with a brick. He flinched, turning away from the light, rewarded with the dull ache and pain that told him that his wounds were fairly fresh, and that jerking anything around wasn't a good idea. "Commander! Can you hear me? Hey, someone get a litter over here. I need a medic, right now!"
Those words, those simple words, sent a rush of relief through him, though his mind remained foggy and he didn't grasp quite why it did. "Wh...what..." he managed to croak out.
"Sir, we're going to get you out of here. The fight is over sir, you did it! We're getting everyone off the citadel now, but we've got to get you looked at. Don't try to move, this beam on top of you could shift at any minute and you might end up half the man you were."
Trying to absorb all this, his mind flashed back, the image of a child, like a hologram. Something about the reapers...he was doing something...he remembered shooting...with a sudden sharp pain, he felt himself slipping back into the darkness, the void enveloping him.
"Look, Doctor, I don't mean to pry, but that man is probably the most important man in the alliance right now. We've already got infighting and arguments going on, demanding answers on exactly how that man saved everyone's asses," Admiral Hackett said, his eyes fixed on the face of the young female physician that stood between him and John Shephard's room.
Dr. Michel shook her head. "I'm afraid that ten days is just not enough. The man has had severe trauma to his body, and even the implants he carries are struggling to keep him alive. He has lost a lot of blood. He needs his rest. We are doing everything we can, but without more information, without experts, we're not even sure that the implants that keep some of his vital systems alive will continue to function."
Hackett growled and shook his head. "Doctor, you tell me exactly what you need, and I promise you I'll get whatever resources I can muster. But that man needs the best. I don't want him dead because we didn't try."
Dr. Michel nodded. "I owe that man my life, probably, twice over. I am doing all that I can, but without more, I cannot guarantee-"
"Perhaps I can be of assistance, Doctor." A female voice said from the entrance to the infirmary section. "I made my way here as soon as I found out what had happened, though I admit I had a bloody impossible time finding this place."
Hackett turned to see the raven haired Miranda Lawson striding confidently towards them. Her features seemed haggard and worn; although given what Shephard had reported happening on Sanctuary, he wasn't surprised. "Ms. Lawson, I'm afraid this isn't-"
"Admiral, my team and I at Cerberus rebuilt that man. I know every detail and every implant he has. If anyone can help your young doctor, it's me."
Dr. Michel nodded. "I remember reading about the miraculous treatments you used to bring his body back to life. If you believe you can help him, then I would be most grateful."
Miranda nodded. "Your infirmary looks advanced enough, Doctor. I'm pleasantly surprised to see it didn't get destroyed during the fighting."
Hackett had to agree. The base was one of the last few complexes the Alliance Military had left that had escaped the fighting. Buried deep within the Himalayas, the facility was deep underground and isolated, a research and development base used by the military's scientists and home to the initial stages of the Crucible project. "Ms. Lawson, I am having the very same engineers and scientists that worked on the Crucible recalled here to begin research and development to help us replace what we've lost. I'll see to it that any equipment we can scrounge and medical equipment or resources you require are sent here."
Miranda turned to look Hackett in the eye. "Did the Cerberus facility survive? I had heard that Shephard and the Alliance seized it."
"The Facility survived, but it was heavily damaged. What do you need from there?"
"There are no doubt stored records of our project to bring Shephard back to life. I'm going to need everything we can find in order to repair the damage. Also, I'm going to need any specialists on microcybernetics and nanotechnologies sent here right away. Now, Dr. Michel, can I see our patient's chart?"
Dr. Michel nodded and handed over a data pad displaying a layered view of Shephard's body and lists of injuries and vital statistics. "These look promising. By these numbers, the basic devices are still functional. We'll have to run diagnostics on them and initiate their self-repair routines, but that's not too difficult."
Admiral Hackett clenched and unclenched his fists. Once again he found himself unable to do much more than play a backseat role as other people's lives hung in the balance. He turned away from then, looking out of a window with a holographically-simulated nature scene, giving the underground facility the appearance of being somewhere lush and tropical. He turned back to the two doctors and rubbed the bridge of his nose. "Ten days later and this hasn't gotten any easier. Dr. Michel, please alert me if his condition changes at all. Ms. Lawson-"
"Uhm, that's Dr. Lawson, actually." Miranda corrected him.
"Dr. Lawson, I'll have everything I can send coming your way. Now, I presume that you'll have work to do and I'm in the way."
The doctors both smiled apologetically and nodded. "Don't worry, Admiral, we'll see that everything is done."
"No, Primarch, I don't have any word other than that Shephard's alive. We've got ground teams scouring for survivors from that battle, the same as they're looking all over earth for any survivors. If Garrus is alive down there, we'll find him." Hackett said wearily. He sat back in the chair behind his stateroom desk and nodded reassuringly to the Turian.
"You'll forgive my pessimism, but to the Turians, Garrus Vakarian is just as important as Commander Shephard. The entire team that accompanied Commander Shephard are heroes and we owe it to them to find them and do what we can, if they're still alive."
"All of the crew that weren't accompanying Shephard were on the Normandy when we ordered all the ships out of the system. We're trying to track down their trajectory through the various navigation and communication arrays we have, but it's proving difficult with the relays offline. If the ship survived, it will have activated its automatic FTL transponders and the beacon installed as part of the quantum entanglement system. Our own quantum systems were heavily damaged during the attack, so anything longer-range than ship to ship is out of the picture right now."
"Well, the good news is that you have a fleet of usable ships and brilliant minds still capable of helping rebuild in the aftermath. I have also already spoken with the Asari and Salarian councilor. They are equally concerned that with all of our forces being so badly decimated by this war, we find a way to continue the Alliance between all of our races. It is important that we protect the weak worlds and bring needed supplies to those worlds."
"I have talked with the other senior officers of the Alliance – the most senior officials left representing earth with the destruction of the Parliament – and we're more than willing to agree with any reasonable agreements to extend forces and support to other members of the alliance. Your races helped Earth when it was most needed, and we owe it to you to return the favor."
Pirimarch Victus nodded. "We appreciate everything that Earth did on behalf of our worlds to allow us to make the sacrifices necessary for yours. I don't think anyone will argue that Earth sacrificed greatly to save all of us, and I don't see any reason why a true alliance between our people is impossible."
A new window appeared on the display of Hackett's control panel and he frowned, peering at it. "Primarch, the Asari representative would like to speak with me. May I have her join this call?"
The Primarch showed a look that seemed surprised, and then nodded. "Of course, Admiral."
Hackett wasn't a politician and playing the game of politician was worse than waiting for the arrival of the Reapers. He'd believed Shephard ever since his first reports of his findings came across his desk. Now, however, he'd inherited the duty of representing Earth as a senior official, and he could understand Victus' own discomfort at being thrust into the world of politics straight from the battlefield. He tapped a control and activated a second display showing the lithe, shapely form of the Asari councilor. "Madam Councilor. What can I do for you?"
"Admiral, Primarch. I wished to extend the thanks and support of the Asari people to Earth for their invaluable efforts to save all life in this galaxy. We feel that it is most important-"
Hackett held up a hand, cutting her off. "Primarch Victus and I were discussing that, Councilor, and you can count on the support of Earth to aid in security and cleanup, and a full participation in a unified Alliance between our peoples."
The Asari looked as though a great amount of her anxiety had been lifted from her shoulders. "Well, then, I am pleased to hear that. Surviving members of our culture spread across many of the worlds have reported in that situations on many planets are deteriorating, and without a strong central government that can provide leadership, I'm afraid what wasn't lost to the reapers will, for many, be lost to infighting and outright civil war."
Hackett stroked his chin thoughtfully, his eyes narrowed. That was grim news indeed, if accurate, since without the relays, travel time between stars no more than a few hours apart before now stretched into the weeks at the fastest speeds their ships could muster unaided. Getting forces out to planets that broke out into war would be far from certain to arrive in time to prevent a war, or worse. Races that lost much of their planetary resources or saw their worlds damaged beyond habitability would find themselves looking to their neighbors as a solution, and attempted colonization would turn ugly if not handled properly.
"We've opened our world to the Quarians and Asari for permanent habitation, and are working with the Quarians to begin identifying areas that meet their needs for food production and settlement until we're able to reactivate the relays, but it's still early and we're still picking up the pieces."
Primarch Victus nodded. "I've had word from Palaven that the damage is severe. Systems necessary for processing waste and food are heavily damaged and it will be some time before we can support the full population of Turians. I've spoken to Urdnot Wrex, and things are stretching thin with the cohabitation of Turian and Krogan now that the war is over. Several flotillas of Krogan ships have left for Tuchanka, and are reporting an estimate of 3 months travel time at their fastest speeds. Wrex is, however, offering to allow Turians to settle in parts of Tuchanka until we can reestablish all of the necessary services on our world."
"All species that are members of our Alliance are welcome to settle on Earth for the short term or long term. I have no problems with sharing our resources since we're going to need everything we can get to rebuild." Hackett said, standing and walking over to a small cabinet. He removed a bottle of scotch and poured himself a glass, then returned to his chair and sank into it.
The Asari nodded. He noticed the lines on her blue face, clear even in the holographic representation, and the fatigue that plagued her eyes. "It's only been ten days, Councilors, and we're going to be shaken up for a while. All we can do is rebuild and try to put the pieces back together now that Shephard's done his part."
"I agree, Admiral. We all appreciate what the Humans have offered to do now that this war is over, and it is clear to everyone that without such an intimate knowledge of Humans, we sorely misjudged your species. I promise you that the Council will begin immediately trying to work out the arrangements to formalize an alliance." The Asari said, smiling softly.
Hackett nodded. Primarch Victus leaned forward, his arms resting on the edge of a desk Hackett couldn't see. "For now, Admiral, we'd like to ask you to take command of the combined fleet. We'll need to begin working on repair facilities and do whatever we can to prepare aid and security forces. I trust you're already working on the Relay problem?"
"I've recalled and settled a facility with the direction to begin developing better travel systems and figure out how to get the Relays working again. The Prothean archives we were working with before the invasion contained the research data they collected on the Relays. Since they were able to replicate the Relays and create the Conduit, I'm hopeful that we can pick up where they left off."
"Understood. Thank you again for listening to us, Admiral. Let's have a drink sometime when it's less formal." Victus said, nodding in respect.
Admiral Hackett sat at attention and nodded. "Will do, Primarch. Hackett out."
He touched a control on his console and disconnected the conference. Rubbing his eyes, he sank down, feeling the weight of a galaxy suddenly pressing down on him again. His eyes drooped from fatigue, though he felt as though he had barely begun working. He picked up a data pad showing reports of ship status and rescue efforts, scrolling through them.
With a long sigh, he tossed the pad back onto his desk and stood, pulling off his jacket. He just couldn't work, suddenly both tired and relieved that the worst decisions and problems he faced was with the continued survival of and rebirth of galactic commerce and safety, not an alien threat that could wipe them all out with a thought. He threw himself on his bed and closed his eyes, dropping off into fitful sleep.
John looked around himself and saw the forest of shadowy trees, figures of men and women no more than wisps on the breeze that circulated between the trunks, moving branches in silent undulations. He frowned, recognizing the landscape as the dreams that had plagued him during the long months he'd worked to stop the reapers. Ahead of him, he saw the outline of the same little boy. "I destroyed you. You and all of the Reapers."
The boy nodded. "Yes. We are gone. Your choice was not unexpected, but it was disappointing that you would not see reason."
"Your reasoning is based on your own fear. You feared destruction at the hands of synthetics so much that your own race created synthetic masters to prevent such a future. The irony of that certainly can't be lost on you."
"It is an inevitability that synthetic life will destroy organic."
"The Geth only fought their creators because their creators feared what they had become and acted irrationally. If Organics recognize sentience and accept that synthetics are no different than Organics, with the same rights and respect, then the outcome may be far different than you think." John said, shaking his head. Was he still here? Stuck on the Citadel with a Reaper in his mind?
"What you propose is possible, but it represents chaos. The outcome is uncertain. We have observed what happens when Synthetic life becomes greater than Organic life, and thus the cycle was created."
"You'll just have to accept that Organics don't like to be told what to do, or to willingly die for an abstract cycle that is based on the fears of another species. Life is chaos. It always has been, and control is just an illusion. Order is an illusion. We will make our own mistakes, and we will fight our own fights. We don't need anyone to play god and take that decision away from us. We embrace chaos and we embrace the struggle against it."
"Then you will lose."
"But we won against you. We stopped you. Millions of years of intelligent life working together to stop the cycle imposed on us out of fear. We won't give up without a fight."
"So you have shown us. We underestimated the will of Organics to win, and we lost because of that. The Crucible showed us that Organic life could not be contained and shaped any longer."
"So what are you? Is this a dream? Am I being indoctrinated and is all of this in my head?"
"No. You will remember in time what happened, but you destroyed us. I am merely a memory, a dream imprinted on your mind to serve as a warning in case we failed and were destroyed. You bear the burden of saving Organic life, but you also bear the burden of knowing that the chaos that follows will have been your doing."
"I will gladly accept that burden. Now get out of my head."
John groaned and opened his eyes. They felt heavy, and the pain returned as he found himself staring up at a metal plate ceiling. He frowned slightly in confusion. He had just been…there had been a Marine over him. He remembered that. Was he still there? Where was the Marine?
"Well look who's awake." A gentle feminine voice said as a face leaned into his line of view.
The face was familiar but his vision blurred. He licked his dry, cracking lips and spoke in a hoarse voice. "Where am I?"
"You're in a hospital, John. I'm surprised that you're even awake, actually. The damage to your body was, once again, extensive." Miranda said, straightening up, crossing her arms. Her black hair was pulled back in a ponytail, her Cerberus uniform replaced by a doctor's coat and simple slacks.
"How long have I been out?" John managed to croak.
"The better part of 3 months now, John. Your body took quite a beating and you needed rest. I daresay you earned it." Miranda smiled.
John had to smile back, though he felt weak and out of sorts. He'd only ever seen her with tension and stress covering her features. Now she looked serene, relaxed. He thought back, remembering the last time he'd seen her. She had killed her father, saving her sister and stopping one of Cerberus's most powerful supporters in the process. "You look good, Miranda. How'd you get here? Where is here?"
"You're on Earth, in an Alliance hospital. I've been put in charge of your care, and believe me, you're lucky I had come to see if I could be useful to the Crucible project after getting Oriana to somewhere safe. You truly were badly hurt, John."
"Well, you pulled my ass back from the brink of death once, Miranda, if anyone could save me, you can."
"Sweet talker." She said, smiling again. "Believe me, you've got a long way to go."
She leaned down and, in an uncharacteristically personal fashion, kissed his forehead. She straightened and turned to leave the room. "Oh, you might want to know, I heard from Admiral Hackett. The Normandy and her crew are alive. They crash-landed on a planet about two months' travel from here and are making repairs."
John closed his eyes and visibly relaxed. He hadn't know that they'd been in danger, but then, he still didn't remember the details of everything that had happened on the Citadel or the events following. He heard the telltale noise of a Geth and slowly turned his head. "A Geth? I thought the blast from the Crucible destroyed all synthetic life?"
"Shephard-Commander. It is good to see that you are still with us. When the Geth were joined with the Old Machines, we were privy to their own analysis of the Crucible and its function. It was not unknown to them. When we were freed of their control and were allowed to join the work on this device, we made the necessary modifications to target the Old Machines specifically. We could not allow them to terminate more life in their bid to control the decisions of Organics."
Shephard nodded. Logical. The Geth had been the closest to the Reapers, linked to their consciousness and, presumably, the control of the Citadel and its own AI, giving them insight he had wished he'd thought to consult before initiating the last battle.
So many questions flooded his mind then, concern for his crew and those he loved flooding him along with a wonder of what would happen now. The feelings overwhelmed him, and he closed his eyes as the room began to spin. "I think I need to sleep some more."
Miranda nodded. "Your body is weak, John, and you'll need to rest as much as you can. I'm afraid that things aren't perfect, and we'll need your strength before this is all over. But for now, we need to get you mended."
John closed his eyes after seeing hers. There was something there that had never been there before: hope.