-Please read the Author's Note before the story-

A/N: This is a rewrite of a the fic 'Decision and Visions', the post Mass Effect 3 fic I was writing before I heavily researched the Indoctrination Theory for the game's ending. This begins with the Destroy Ending, the one which Shepard is alive because she refused to succumb to Indoctrination; everything after Harbringer's beam – based upon the Indoctrination Theory – happened in Shepard's head. The final push the Reapers made to try and control Shepard. The Indoctrination Theory does have its flaws; are the Reapers destroyed, what happened to the Citadel and Mass Relays, are your teammates alive or dead after being struck by Harbringer's beam? Considering you have to have the highestEffective Military Strength score for the true ending, it is my belief that the forces Shepard amassed would have been enough to destroy the Reapers at Earth and destroy the Citadel; and since the Citadel and its Keepers are linked to the Reapers and Mass Relays( as it is all Reaper technology), destroying it would destroy the relays and the Reapers. This brings into question what the Crucible was and how it was used – I would like to interpret it into a way that keeps the relays intact and does not kill all synthetic life(given how the god-child bold faced lied to Shepard about how the Destroy choice would kill her, when it clearly did not – it could have been lying about the synthetic part, to keep Shepard from making that choice).

This story is based upon the Indoctrination Theory, however, a lot has still been left to interpretation and this is how this idea – this story – came to be. All reviews are loved, and by far appreciated; I just ask that you be gentle – constructive criticism is different than flaming. Flaming will be ignored so please, don't bother. I ask that if you don't like it, please just leave without comment.

Without further ado, the beginning to After Our Darkest Hour.

Disclaimer: Bioware.

After Our Darkest Hour

Chapter One - Surviving Against All Odds

"Shepard? Shepard can you hear me?...Ugh."

"You okay, Kaidan?"

"Fine, don't worry about it. We need to find Shepard."

"We will. We won't leave her here, not after everything we have been through."

"Damnit. Shepard? Shepard!"

Her head was pounding, as if someone had been smashing it against a wall. Her body felt worse – heavy, aching, shooting pains all over. Her ears were ringing, but she swore she could hear voices amongst static; was it her radio? She opened her eyes slowly, only to see nothing but rubble and darkness. Next she tried to move, but a quick assessment from the soldier alerted her to the fact she was half buried under heavy pieces of concrete.

That…couldn't be right.

She had been limping toward the panel her Alliance issued N-7 Eagle clutched in her bloody palm. Her head had been buzzing, insidious whispers telling her that this wasn't the right choice, but she had pressed on. Anderson had said destroying them was the only way; she had been fighting this war too long this way to let her beliefs slide. There was no controlling the Reapers – just their destruction. As she had grown closer the red-hued panel, her body had become lighter and she had straightened, shoulders back, head held high, pistol lifted and aimed directly at the barrel of the panel. The whispers turned to screams and she grit her teeth, pulling the trigger – once, then twice, again and again. Even as it exploded in her face, she pressed on. One final explosion and then there was nothing but darkness, her head suddenly whisper free as she floated, feeling as if – at last – they had finally won.

She could not have survived the impending explosion of the Citadel. If she did survive it, she still would have been left in space with no helmet, falling through the Earth's atmosphere and plummeting for the ground from the sky.

No…she shouldn't be alive. She shifted and then bit her lip, biting back a groan of pain. Spirits, but did it hurt. She hadn't expected to survive; the odds had been stacked against her.

"Lola…" A soft sigh. "At least she went down fighting."

"She is not dead! Stop talking like that damnit, and move that damned rubble!" A groan and sharp intake of air, that was exhaled on a shuddering breath.

"Kaidan let me look at that. I have some medi-gel."

"No! We can't afford to stop looking. You saw how injured we were by Harbringer's beam…s-she could be far worse off than us, we have to find her."

"Kaidan…" She sighed his name, her heart giving a faint flutter within her chest. She had distanced herself from all others after surviving Mindoir and then Akuze; it wasn't just the survivor's guilt, but the ominous feeling that she brought death to all those around her. Then Kaidan had come along and pulled her into something she could not deny – ominous feelings and regulations be damned. Even when he had turned his back on her after her resurrection, and even after they had held each other at gunpoint because he didn't fully trust her, she couldn't deny what she felt for him. Through some miracle, while others continued to die around them – Ashley, Mordin, Thane, Legion – they had managed to stay alive. It was a heavy weight off her shoulders to hear his voice, to know that he had survived.

"Did you hear that?"

"Was that Lola? Damn! She is a tough shit, I'll give her that."

"Now is not the time Vega! Shepard, Shepard? Can you hear me? Please, say something – anything."

She coughed, her chest shuddering with the motion. Her throat was so dry. How long had she been laying here? "I'm h-here…"

"Damnit Shepard, you made me promise to be waiting for you and I am! Where are you? Can you tell us where you are?"

"It's…dark. I'm…" she coughed again, her body tightening up as she tried to readjust, lying buried beneath all this debris making her stiff. "…buried…l thought…I thought I made it to the beam…"

"Negative, Commander. Harbringer's beam brought us all down. Damn – a couple more scars for the rebel persona."

It was like Garrus to say something almost uplifting in a moment as bleak as this. "How…long ago?"

"Through the night – it's midday now. We've been searching the rubble of the conduit for you. Only you seemed to be in the thick of it."

"I remember…Harbringer's beam…I was so close." She lifted a hand, grasping at the piece of concrete that lay over her left shoulder, using all her remaining strength to shove it off. She groaned, her head lolling back as her chest heaved.

"Shepard! Are you alright?"

"F-fine, Kaidan…I should be close to where the beam hit us…" She heard something, sounds of pieces of concrete being hefted and moved around. Shifting of the rubble around her. "I…can hear you." Dizziness swarmed over her, blackness teasing at the edges of her vision even as she shut her eyes.

"She's close! Get a move on!"

Kaidan's heart was pounding like a jackhammer in his chest as he lifted a piece of rubble and threw it aside. She was alive, damnit, and they had to find her before that changed. She wasn't answering them now and he feared the worst. Vega, Garrus, EDI, and Javik were helping, while Liara and Tali helped coordinate medical supplies, as well as helping fallen soldiers as they were uncovered. Most were dead, but Kaidan knew if anyone could survive this, it would be Shepard.

"Move faster!" He yelled out the words, his chest heaving with the physical strain. The extent of his injuries had left him without his biotics, but he wasn't about to let that stop him.

"Yelling at us isn't going to make finding her easier," Vega grumbled, though he was quick to shut his trap when Kaidan's amber glare fell upon him.

"That isn't going to help matters," Garrus whispered to Vega, who merely grunted in response. "If someone you loved was under all this –" the Turian's mandibles tightened as he lifted and tossed a piece of concrete out of his way – "nothing would stop you either."

"The odds that she is still alive are slim at best." Javik said after a moment.

Garrus hissed at the Prothean, "that won't help either! Just shut up and keep moving. Shepard is known for beating the odds."

Kaidan sighed almost gratefully at Garrus' interruption, his frustration welling up in waves of anger at the conversation; he didn't care what the damned Prothean thought of odds. He was going to find her, even if he had to be here, moving rubble and debris, for days on end. Even as his body was aching, his head throbbing, he couldn't bring himself to stop, even for a moment for Liara to check on him or down a bottle of water. He couldn't stop until he found her.

"Over here!" Vega nearly screamed the words as he chucked aside some debris; there, he could see the distinctive color of Shepard's unique armor on her boot – how could anyone miss that black, red, and white armor amongst a sea of greys and blues?

Kaidan dropped the concrete he held and ran across the stretch of debris to where Vega was digging frantically, pulling piece after piece away. The biotic Major fell by his side, Garrus joining in next, both helping uncover the Commander's prone body. His heart nearly stopped in his chest, his hands trembling; she was so still.

Please, please! She can't be dead, not after all this! They couldn't have come so close, only to fall short at the finish line – he wouldn't allow it.

"She's not breathing!" Garrus exclaimed, panic edging in on his two-toned voice.

"No!" Kaidan denied if vehemently as they carefully removed her from the rubble and moved her to flat ground. She was covered in blood. Her armor was melted to her skin in places, her hair dingy and matted with dry blood. Her lip was split, a gash above her eye through a dainty eyebrow. Kaidan's eyes fell on her chest, waiting for the lift and fall of her breastplate; when it never came, he shoved them aside and started chest compressions. It had only been three minutes, at max, since she had stopped responding; there was still a chance.

"It is unlikely you can revive her, Major," EDI informed him as the rest of the team gathered around save for Javik.

"I will," Kaidan hissed the words and pinched Shepard's nose shut, bending down to lock his lips to hers, breathing for her by giving her his air. Then up again for compressions. It seemed hopeless, but then Shepard gasped, her whole body arching as she dissolved into a fit of coughing. Liara was on her in an instant, applying medi-gel to what she could, as Shepard fell back lethargically.

Kaidan tapped into his radio, activating the link with the Normandy. "Joker, do you copy?"

"Loud and clear, Major."

"Get the Normandy down here now! We found Shepard! We have to get her to Dr. Chakwas immediately!" He tried to keep the panic from his voice, but it was there, lacing through his deep voice without subtlety.

"ETA two minutes."

"Kaidan, you need to pick her up, but be careful. I have done all I can for now." Liara laid her hand on his shoulder, jerking his gaze back to Shepard.

He nodded, slipped out from under the Asari's hand, and leaned down, slipping his arm beneath her head and the other under her knees. With a grunt, he lifted her up, trying not to panic as her head lolled against his shoulder. "I got you, Shepard." He whispered as he kissed her brow. "I am not letting you go, I promise. Just hang in there." Holding her tightly to him, but mindful of her injuries, he trekked away from the rubble toward the crest of the hill where the Alliance soldiers were gathered. In the distance he saw the Normandy dropping low, heading toward where they were, and his grip on Shepard tightened.

"Hang in there."

"Shepard is waking."

Shepard's brows drew together tightly, EDI's voice filtering through the darkness to lure her forward. Her eyes shut tighter, clenching shut, before she hesitantly let them flutter open. Light blinded her and she winced, arm rising slowly to shield her gaze from the offending lighting of the med bay.

"Shepard?" She winced slightly uncertain as to why when someone stopped her arm, taking her hand and lowering it to hold it in theirs. That voice sounded familiar and she worked through the webbing of blurriness that made it hard to see. She shut her eyes and took a deep breath before opening them again.

Kaidan leaned over her, grasping her hand as his own trembled. They had come close to losing her twice already and he worried she would relapse, even though both Chakwas and EDI assured him that, with time, Shepard would make a full recovery. Her eyes found him, those beautiful nearly silver orbs drawing him in and holding him prisoner as they had from the very beginning. Her lips twitched, then pulled up into a slight smile. Her other hand lifted and found his cheek, stroking it gently.

"Kaidan…you found me…" She whispered the words, and nearly choked on them as she trembled; she was not one to show fear, but even she had her moments of weakness. Of all people, she was entitled to them.

"Always." He glanced up to see EDI and Chakwas discreetly leave the med-bay, before dipping his head down to kiss Shepard's trembling lips. It was light, brief, and achingly tender. It was the perfect kiss, one he had wished for years before he met Shepard. Never had a woman held him so enthralled. To have lost her once had nearly killed him as well, to have nearly lost her again was maddening. He withdrew slowly and took his free hand, running it gently over her hair. "You scared the shit out of me, Shepard."

"Sorry," she chuckled softly, shaking her head. "What…what happened, Kaidan? I…I saw so many things after Harbringer's beam and…I wonder if I've finally lost my mind."

He sighed softly and sat back in his chair, though he kept ahold of her hand. "No one reached the conduit beam, not after what Harbringer did to Hammer. Hackett docked the Crucible and it fired a red light. It enveloped everything. I…I wasn't recovered myself until after the beam fired, but Hackett made a report to the entire Alliance that the Reapers fell to the beam and the Citadel, along with the Crucible, detonated. Surprisingly, the relays seem to be intact. Except for our friends, the rest of our alien comrades have retreated to aid their home worlds in their rebuilding efforts."

"I really must have been going mad…" She groaned and took her hand, scrubbing both of her hands over her tired face.

Kaidan leaned toward her, sliding his hand in a gentle caress over her hair again. "What is it Shepard?"

"I…I don't know. I thought…I thought I had made it to the beam, though I was severely injured. The Citadel was lined with bodies but…they didn't look right, like dolls almost, husks maybe. Anderson somehow made it and I found him and the Illusive Man. I shot Anderson…" her voice trembled. "but then I shot the Illusive Man; he'd been controlling me somehow and my head was buzzing, I couldn't think. Anderson said the Crucible wouldn't fire…next thing I knew I was in an area I had never seen, some weird AI telling me the choices I had in beating the Reapers…control them or destroy them…" She broke off in nearly bitter laughter. After a moment she sighed. "But then I woke, under all that rubble…it must have been in my head…"

"Shepard…" He stood and slid her over gently. He lay beside her, drawing her into his arms and holding her against him as she shuddered, subdued sobs desperately trying to make their way from within her. Only one or two times before had he seen her cry – she was so strong – but she deserved a moment to break down and be human.

"On top of the dreams…the whispers…the oily shadows." She shuddered. "Am I going insane, Kaidan?"

"No, Shepard. It's okay, it's all okay. Except for a few more scars, we all made it out alive by some miracle or another." He said the words with conviction, convincing himself just as much as he did his best to convince her. "It's over now."

"Kaidan, is Anderson…?"

"He's alive, Shepard…but he was nearly dead when we found him, like you. He's in the temporary ICU. As is Cortez." He stroked her hair, pulling her head to lie against his chest to find comfort in the slow, calming rhythm of his beating heart.

"How bad off was I?" She sighed softly, taking comfort in his arms. She had come so close to losing this forever.

He shuddered, his arms tightening around her, his nose burying itself in her hair. "When we found you…you weren't breathing. I had…I had to give you CPR. We brought you onto the Normandy and Chakwas nearly lost you twice. You were covered in blood…bruises…cuts…scrapes…your armor was m-melted to your skin in place…" He choked slightly and trembled. "It was too close, Shepard. I came so close to losing you again…God, Anvi, I don't know what I would have done without you. Please don't do that again."

"I love you Kaidan." She pressed her lips to his frantic pulse. "I would gladly give my life to save you, you know that."

"Hey, hey. None of that, please," he chuckled into her hair. "I love you, Shepard. Don't you dare do that again, and that's an order."

Shepard smiled and closed her eyes, leaning into his hold and taking comfort there. It felt right, but the fragments of her dream were there, still taunting her mind of things she were certain had happened and yet, had not. It had felt so real…but as she lay there, wrapped up in Kaidan's arms, she could be thankful that it had not been. That this, this was her reality and not the warped one that had turned her world upside down and destroyed her.

"Aye-aye, Major."

A/N: So that is the rewrite of the first chapter; as I said, besides the beginning and some…other things, the story will remain the same. Some parts will have to be reworked, given the Citadel was destroyed, but I am hoping this will be a good story even with the changes. A couple of you have voiced displeasure in my choice, but as an author, I have to stand behind it and not falter. All reviews are appreciated, as always. And thank you to any of you that have given this fic a chance.