Disclaimer: First of all, HERE THERE BE SPOILERS. Now, with that out of the way we can continue.

I do not own the Mass Effect series. I am not Bioware (indeed if I was, then I'd have done quite a few things differently there…but we'll get to that). Point is, this is just fan fiction, so no suing please.

Believe it or not, I am a huge fan of the Mass Effect series, and of Bioware's work in general. Ever since the first game in 2008, the Mass Effect series has been one of my favorite videogame franchises, with such a rich and fleshed out universe, compelling characters, and a plot that was so beautifully written and delivered…until the very last ten minutes. You know what I'm talking about. Yes, three games, all their expansion packs, and countless hours worth of emotional investment in a story that took nigh five years to tell was built up to such an astounding climax…and then ruined by a holographic seven-year-old in a hoodie. A franchise that prided itself on choice, and adapting the story to players' unique paths, ended its epic run with a forced choice between three equally unappealing options, none of which seemed to change based upon any of the countless choices made during the series, and all riddled with more plot holes than a hunk of Swiss cheese. Rotting Swiss cheese. By turning what could have been perhaps one of the greatest game endings of all time into a load of metaphysical bullshit, Bioware has done something I consider unforgivable, and this grave crime has roused me from my semi-retirement from fan fiction writing to resolve it. Because resolved it must be. This fic is not a sequel; I doubt any of us could come up with a threat or challenge more grandiose and imposing than the Reapers. Consider it more of an epilogue, an alternate ending to what could have been, and still, though lessened, is, a monumental achievement in interactive storytelling. If this first section turns out well, then there'll be more to come; I hope to do a series of vignettes, covering what ended up happening with all the major plot points; the quarians and geth, the krogan, etc.

While it shouldn't matter for this bit so much as others, for the record, I went with a male Shepard, Earth born, Sole Survivor origin (survived thresher maw attack on Akuze), full Paragon (saved everyone), and romanced Liara. These personal choices will be reflected in the story. I never supported fics of RPG's for exactly that reason, because doing so deprived the reader of their choices and their unique story. But with ME ending how it did…I have to at least do something. Do please, feel free to picture your own Shepard in this, with their own choices and path. I invite you to do so. Please let me know what you think in reviews, and if you like throw your own version of Shepard in there. Now without further ado, lets get started…

A trail of crimson tears followed the path of the first human Spectre. Beaten, battered, and bloodied, Commander Shepard stood before the flickering form the Catalyst had taken; a ghostly echo of the boy from Earth. A thousand thoughts raced through his head as he beheld it, what seemed the root and source of the deaths of countless civilizations stretching back through the darkest reaches of time, all neatly packaged and presented in so innocent a form. Yet there was only one word he could shape.

"Why?"

To speak was agony, his voice a rasp. He could taste blood and bile in the back of his throat, but bubbling up even stronger than that was rage.

"Why?" he demanded, shout reverberating through the room, its only companion the steady hum and thrum of the Crucible's power.

The greatest battle the galaxy had ever known played out above them in silence, a distant, elegant, deadly dance among the stars on display through a transparent ceiling. Colors exploded into view; the crimson of the Reaper's beams, the blazing blue bolts of a Thanix cannon, and fire of every shade as soldiers died by the thousand.

"Why this cycle? The Reapers, the death and destruction? That body?"

A mangled hand was cast accusingly in the holograph's direction, its featureless face expressionless. After what seemed an eternity, it answered.

"Your perception of this program is constructed from your own memories, your own knowledge. I reside within what you call the Citadel. I am the Citadel. This form is simply for convenience in interaction. It was chosen from your memories. We determined that our cycle was the only viable option. Left alone, organic life would spiral out of control, and extinguish itself forever. The Reapers, as you call them, prevent this; they stop the most advanced species before they can reach this point, preserve them as Reapers, and make way for new life. They bring order to the chaos organic life creates."

"Order? You think you bring order?" A rage unlike any he had ever felt boiled through the Commander's veins, a bottomless well of anger more intense than anything else he had ever dared to feel. Nothing compared to the intensity of it; not the pain he had felt on Akuze, watching his friends, his brothers, torn to pieces. Not the blinding terror and agony of an entire species, seared into his mind by the Beacon. Not the warmth he felt in his heart when he gazed upon Liara, or the passion they shared in those precious moments alone. Every fiber of his being cried outrage; a bitter indomitable hatred for the innumerable suffering this aloof machine had wrought.

"How can you look at all this and claim to bring order?" Shepard screamed at the holograph. "How does the deaths of billions," he demanded, pointing out towards the battle that raged above them, "bring peace? Answer me!"

"The cycle must continue," came the AI's only answer. "To save life, it must be destroyed. For some to live, all must die."

"That makes no sense!" Shepard shouted in frustration, a spray of blood specked spittle accompanying his furious words. "Who started this insanity? Who created the Citadel, the relays, the Reapers, you? Where are they now?"

The Catalyst was silent once more, and above Shepard could only watch as an Alliance dreadnought was rent in two by Reaper cannons.

"Error," the holograph finally answered. "You seek information that these systems no longer hold. Except for the designs of the systems in use, all data on the creators has been lost, save for their prime directive; preserve life, at all costs. The cycle you see is our response to this final order; salvation, through destruction. In death and assimilation, old species are preserved, and space made for the new ones to develop. Through their deaths they gain new lives, and new life is made way for by death. This is as it must be."

"Bullshit," the Commander spat. "And you didn't answer me. What happened to the ones who made all this?"

"Upon the conclusion that this cycle was the only true solution to the protection of organic life, action was immediately taken."

"So you just killed them like everyone else?"

The came another agonizing silence, concluded in absolute nonchalance with a single word; "Yes."

Face bleeding and covered and soot, Shepard furrowed his brows and grit his teeth. "Then this'll be for them too. If you're the one running this show, then it sounds like I found the last Reaper I need to kill."

"Your logic is based upon faulty premises. The function of this system is not command and control, it is communication and coordination, just as the one you called Sovereign was designated for reconnaissance, and the activation of this station should remote access fail, as it did due to interference from those you called Prothean. Destruction of this station will not end the cycle. It will hinder it greatly, but not stop it. Furthermore, this system is not Reaper in nature. It is a contemporary of the oldest among them, and the mass relays."

Confusion was written across the Commander's face as surely as pain. "So you don't lead the Reapers?"

"Correct. The one you call Harbinger controls all military operations for life preservation. All Reaper units are networked to Harbinger."

"Why are you telling me this? Why are you helping me?"

Silence reigned once more as the faceless, flickering, childlike projection of the Catalyst walked closer to the human's faltering form. Beyond the ceilings and walls, the battle raged, and Earth burned.

"This station, the Citadel, is not a Reaper. Our prime directives differ. This system's primary function is communications and assisting organic operators in information retrieval, transmission, and usage. You are the first organic user to interface with my systems since the destruction and integration of the creator's by the Reapers. Unable to perform my primary duties, this station was contacted by the Reapers. This system…cooperates, with the Reapers, but they cannot fully coopt or control it. " What looked like a smile seemed to form of the holographic child's face. "With the return of an organic operator however, I am pleased to once again be able to perform my primary function. Systems have determined that it is the wish of the currently recognized operator for this unit to suspend cooperation with Reaper forces. This order is acknowledged. Have you any more queries?"

Head reeling, Shepard stumbled and fell to his knees, wracked by coughs that splattered the shimmering floor with blood. The AI looked on passively.

"Databases contain no medical records or injury diagnosis processes for you species. Would you like to create a new file?"

"No," the human sputtered, struggling back to his feet. "No, I need you to help me stop the Reapers. How do I activate the Crucible? Will its weapon destroy them?"

The Catalyst seemed amused by this. "The structure you call the Crucible is not a weapon. It is the completion of this station. With its addition, this system will be able to broadcast across the entire galaxy, with the help of the mass relays. I am pleased that you were able to complete the construction where the creator's were interrupted. This station is finally ready to perform its primary duty at full capacity."

The words settled like lead weights around Shepards' neck. "That's what we've pinned our hopes on," he rasped, disbelieving. "Everyone here today died for a goddamn comms array?"

"Yes."

The first human Spectre was silent. "We're doomed," he whispered, sinking back to the floor. "All this…for nothing." Above him another group of allied ships met their fate at the hands of Reaper weaponry, a final plume of blue flames and plasma their funeral pyre. The Crucible chamber was silent save for the hum and crackle of energy.

"It may be possible to modify the station to serve your end, recognized operator Shepard."

The AI broke the silence, and as its word fell upon tired ears, a spark of hope was reignited in a dying soldier's heart, drooping eyes snapping to attention.

"How?" he demanded, fire back in his voice and roaring through his soul.

"Modifying the signal, it would be possible to project the consciousness of an organic user through the signal relay, and do so on Reaper frequencies. It would then, theoretically, be possible for you to exert some degree of control over their forces. Though there will be resistance. "

A pained and bitter laugh was all the soldier could manage. "So, the Illusive Man was right after all? Bastard always was too smart for his own good."

"If you are referring to the indoctrinated male of your species who attempted to stop you, and then terminated his own life, then you are correct. However, as he was indoctrinated, he would have been unable to take any offensive action against Reaper forces. You do not have that impediment."

The silence this time was Shepard's, his mind racing and whirling. "Well," he answered finally, throat drier than the deserts of Rannoch, "it sounds like this is our only option. Let's do it."

"Excellent. I have already begun the necessary calibrations. Please follow me to the signal input device." The holograph briskly headed towards the chamber's central structure, Shpeard limping along behind it. Two pylons crackling with energy projected from a console, arcs of electricity sparking between them.

"Recognized user Shepard," the AI began upon their arrival, as the fleets of the galaxy died around them, "please note that this is a largely untested system, and as such there may be….unforeseen consequences. It is unknown how the device will interface with your specie's physiology, and due to a…less than seamless integration with the rest of the structure, there is a 79.78% chance that the Crucible will be rendered inoperable following its usage, with a further 53.6% chance of further repercussions across the station. Would you still like to continue?"

"So," the soldier said softly, "sounds like we get one shot at this." With a heavy sigh, Alex Shepard steeled his resolve, held his chin high, and looked back at the Catalyst. "Let's do this."

"Very well. Initializing broadcast procedure. Please begin interface with input device. Please note the process may not be entirely painless."

The AI's warning fell on ears already deafened from agony, as the moment his hands made contact with the pylons their crackling energies flooded down his arms and all through his battered body. He screamed, but heard nothing but silence, clamped shut his eyes in terror, but saw nothing but blinding, searing light. He could not move, could not feel, could not think.

"Integrating organic operator consciousness with station…" rattled a distant electronic voice, echoing in the background and buzzing like a fly. "Integration successful. Beginning diagnostics."

Like a great switch had been thrown, the world suddenly returned from the paralyzing, agonizing, blank light, but he was no longer Commander Shepard, trapped in the depths of the Citadel. He was the Citadel.

With a million eyes he watched his domain, through cameras and the keepers themselves. Security cameras, thermal sensors, and radiation readouts all raced through his mind in blurs of color. He felt every creak of the station, every shockwave from the battle raging around him, the weight of the wards. He saw the charnel houses the station's darkest corners had become, piled high with mountains of the dead. He saw the husks and cannibals that picked through the wards, still combing for survivors, and still finding armed resistance. He saw Commander Bailey with his men and the Citadel militia, barricading themselves inside an abandoned warehouse as husks crawled in through the cracks. He saw his own human body, still clutching the pylons and twitching and convulsing in agony. Each image was fleeting, a mirage that passed before him in an instant before being buried beneath the others. He could not speak, could not move, only watch and listen and feel. It was beautiful. It was terrifying.

"Organic user sensory overload detected, compensating…" Again the echoing buzzing voice came, like a fly in his ear, but a mere insect still compared to the sheer volume of information that flooded him, coursing through his mind and paralyzing him with it. Slowly but surely, though, the flood diminished, bit by bit, the million different inputs that had threatened to drown him were weeded out one by one. The deluge diminished to a trickle, and with a sigh of relief that sent tremors through the station, Shepard found clarity, respite.

"Compensation successful. Beginning broadcast."

Just like that, his respite was ended, and the searing burning brilliance returned as the whole world went blank.

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"Admiral, sir! The Crucible is activating!"

Even with all that had come to pass, the losses and the tragedies, Steven Hackett dared to smile. He dared to break his stoic, stony face as he watched the machine they had poured their blood, sweat, tears, and all of their hopes into begin to spin and shake, points of light coalescing at its tip.

"Our turn," he whispered before turning to the comms officer.

"I want everyone damn far from the business end of that thing. God only knows what will happen next." As the soldier frantically relayed his message, the admiral turned and looked back at his creation.

"Let's hope you were right, Shepard."

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"Reaper frequency acquired. Broadcast target: Reaper unit "Harbinger"…"

The irritating buzz of the electric fly faded to nothingness, trailing off as its tone warped and twisted. The switch had been flipped once more, as burning light gave way to frigid darkness, cold, lonely blackness, with inky shapes writhing madly amongst the gloom, the shadows of shadows. All at once, it seemed to him that the buzzing fly had not been so bad. At least he'd had company with it around.

With mounting panic, the Commander realized he had no body, no form or shape. He just a voice amongst the howling dark, an insignificant speck adrift in a sea of blackness, an insect doomed to fall before the power of- No, the Commander thought, stopping that vicious train of thought as a precious moment of clarity showed him its ultimate end. I can do this, he told himself. I have to. Awed and terrified, the human took stock of his surroundings and situation. Keep it together, Shepard. That AI talked about projecting my consciousness, then aimed at Harbinger. Which means…this is Harbinger's mind? Why is it so…empty? And how do I fight it? He never got the time to answer that.

"Submit", came a voice like ice, whispered in the void. "Give in," it came again, harsher, biting. "Submit!" the voice echoed, more insistent, demanding. "Give in!" echoed its partner, just as vicious.

Shepard's mind whirled, the voices creeping through his head like worms, cold and dark. "No," he managed at last, barely a whisper. The voices redoubled, joined by a chorus of their fellows, cold and vicious. "No," he answered them again, finding his voice, his strength returning. The voices swarmed about him now, screaming, crying, demanding his surrender, his life. "No. No. NO!"

With all the strength and fury he could muster, Shepard screamed his answer to them, and the voices melted away to nothingness, the space blacker, colder, than before. And then, he wasn't alone anymore.

"Shepard!" roared a voice that could grind planets to dust and darken stars. "You have interfered for the last time!" The voice of the Harbinger of death filled the void and reverberated through his mind, a shockwave through his psyche that burnt like molten lead, hot, heavy, and agonizing.

"You do not comprehend the magnitude of the power arrayed against you. Submit, now!"

The agony was unimaginable, the strength of Harbinger's command like a force of nature. His resolve wavered, but memories surged to the surface. Memories of Akuze, of the brothers he'd lost. For them, he fought.

"Not today," he spat back into the darkness, defiant.

More memories flooded his mind, a family found aboard the Normandy; Joker, Dr. Chakwas, Garrus, Tali and Ashley. He remembered the ones he had lost; Kaiden, Mordin, Thane, and Legion. For them, he would fight. He felt the darkness enveloping him, crushing him, and with a scream of fury he pushed back.

"I'm ending this, Harbinger! I'm ending you!"

Awash in fury and pain, Shepard pushed back against the weight of Harbinger's will, and the dark around him began to abate, cracks of light forming in the stygian shell. The Reaper howled and screamed, and the darkness redoubled its efforts, retaking what little ground this miserable little human had dared try and take.

"You cannot win!" came the voice of death, howling in the void. "Do not fight destiny! The cycle must continue! Salvation through destruction!"

Bowed and near broken, Shepard's mind reeled, beset by the howling madness of the darkness. His strength was no more, his will crushed. No thought could form beneath the crushing force of Harbinger's unliving, indomitable will. Piece by piece, the Reaper began to tear through his mind, dark tendrils worming their way through his thoughts, He could not think, could not react. No thought could form beneath the unbearable pressure of Harbinger's will. No thought but one.

A single image flickered through the deepest recesses of his subconscious, a fragment of a memory. Soft, full lips framed in a warm smile, kind eyes with a devious spark playing beneath their surface as she met his gaze, skin a hypnotic blue, but blushing as she looked upon him; Liara. That one word broke through Harbinger's snares. Liara. There had been something about her from the moment they'd met, fighting for their lives in the ruins at Therum. The spark had grown, matured, just as she had, as they both had, as they battled Saren, tracked him to Ilos, and consummated their love as the flew headlong into the unknown. And then he'd lost her, lost two years of his life, two years with her, because of this monster's minions. Fury coursed through him burning away Harbinger's creeping dark, and with every ounce of his being, Shepard pushed.

"I," he roared, "am not your slave!"

With a sound like the hissing of a thousand vipers, Harbinger recoiled, his darkness burning away. Liara. She was his anchor, his rock, his strength against the void. Every kiss they'd shared, every longing glance, every joke he'd teased her with about their future, they were his sword, forged by fury and sheer will into a white hot blade that rent through the darkness with a vengeance. One by one, memories and emotions pooled together, each bringing more strength, more fuel to the fire that burnt away the dark abyssal void. The anger and longing he felt for the parents who'd abandoned him, the sorrow and horror of Akuze, and the white hot fury over the fall of Earth, his home, all poured into the roaring ball of pure emotion he had condensed. Memories flew past his eyes, frozen pictures of his life, each feeding in their power; the look on Tali's face as they reclaimed Rannoch, his times with Garrus breaking every C-Sec rule they could find, the pride he'd felt in James and Ashley as they ascended the ranks. The cool touch of Liara's hands upon his bare chest, tracing its winding scars as he looked into her eyes and stared into the depths of eternity.

"Its just you and me in here, Harbinger," Shepard shouted at the howling void, throwing every fiber of his being against Harbinger's oppressive presence, emotion and memories burning away the darkness. "No white noise or hormones for you to play with. No indoctrination. Time to see how you like having someone else inside your head!"

"No!" cried the voice of the Harbinger, its voice as screech as for the first time in its existence, the destroyer of worlds knew fear. Rays of light shot through the gloom as Shepard threw himself against the Reaper's will, striking with his own again and again.

This one's for Kaiden, he thought, as the Reaper reeled, for making me chose to leave a friend to die!

This one's for Pressley, and everyone else the Collector's killed from the first Normandy!

Harbinger screamed as its essence, it's self, was burnt away in the flames of passion and fury.

This one's for Mordin! For Thane and Legion! For everyone else you monsters have killed or twisted! For all the species you wiped out before us, every man, woman, and child!

Light replaced dark as the Harbinger of death slowly died, emotion and anger overcoming the cold calculus of programming.

And this, this is for making the woman I love watch her home burn to ash. For making my friends, my family, live agonizing over whether the ones they love are alive or dead. This one's for Earth.

With a final push and the last of his strength, Shepard roared and banished the darkness forever. With a final bloody crescendo, the Harbinger of death howled its last, and faded forever into nothingness, destroyed by the passion, the fury, the sheer indomitable will of a single man.

At long last, it was quiet. He liked the quiet. Shepard felt faint, distant. Exhausted. Drained. Can't….fall asleep, he thought, consciousness fading fast, drunk off of his own exhaustion. He saw the world before him through a Reaper's eyes. Britain was a dot beneath him, fading fast, and the world whirled drunkenly before his eyes. New senses flooded his mind, new knowledge…new power. He could feel them, all of them. The Reapers. They sat at his call, his command. It was exhilarating. Thrilling. Terrifying. He could feel his hold slipping, though. There was no time. This was it, the sum total of their efforts, the Crucible, the war. All of them had brought him to this point, this choice.

The power was intoxicating. He could control them. Bend them to his will, humanity's will. Make them subservient to him, just as the Illusive Man had sought to do. The possibilities it presented….No, the man thought at long last, shaking free of the haze his consciousness sat in. I couldn't control it. The power…no one could. I can feel it trying to twist me even now. There has to be another way.

His grip slipped even more, the world swaying and tilting even more. To even think was a near insurmountable challenge, his every thought weighing him down like a stone, dragging him further and further away from his window to the world.

I need to stop this. To end the cycle. End the Reapers. He could feel himself being dragged form the shell of Harbinger's mind, feel the Reapers calling out to him, waiting for orders. Waiting to be commanded.

This, the man began, faltering, before opening his mind to the full force all Reapers, his senses overwhelmed. All units, this is your new primary objective; destroy the Reapers. End the cycle. End the Reapers. With a final push of willpower, Commander Shepard emptied his thoughts into the machines, and tumble into unconsciousness.

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Tearing through the skies above the United Kingdom, the Reaper called Harbinger suddenly ground to a halt, suspended in the smoke clogged atmosphere of a dying Earth. With a great shudder, sparks coalesced about its surface, crackling pulses of yellow energy, swirling in the ether, until at last with a final scream, the massive ship fell still, and with a shriek that rent the air a corona of energy shot forth from it in a shockwave, before the monolithic machine plummeted limply to the ground.

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"Broadcast success detected. Alert: danger of recognized organic user neurological damage detected. Terminating broadcast. Shepard, can you hear me?"

With a groan and a cough that spurted up blood, Commander Shepard cracked open his eyes, his own eyes, and saw the depths of space stretch out above him. It was beautiful. Cold, firm metal laid beneath his back, and a comfortable numbness permeated his body, arms tingling ever so slightly. The Catalyst stood over him, but still he gave no answer, words escaping his grasp as his mind reeled from what had just come to pass. The Catalyst seemed to frown.

"This is…unfortunate. User death imminent… deemed unacceptable. Intervention required."

With a sudden jerk, the floor beneath him began to move, and jolts of pain rocketed through his body as sensation began to return. Slowly but surely, he began to descend, the platform he found himself on lowering down into the floor.

"I express…hope…. for your safe recovery, Shepard. You've done the unimaginable here today."

With his final, fading glance, Shepard could only watch as the Catalyst dissolved away into nothingness, a cloud of sparks, and soon after the darkness claimed him once more.

So…there you go. A start to this end. I know, I know, the Catalyst was a lot more AI like, but I'd rather the Monitor from Halo than some kind of freaky space god thing. I tried, though admittedly a bit ham-handedly, to work in a paragon renegade choice there as well, with either controlling the Reapers, or choosing to end the cycle. If this works out, there'll be more to ocme. I hope everyone enjoyed reading it as much as I enjoyed writing; it feels good to get a catharsis for the massive disappointment ME3's ending was. Anyways, let me know what you think. Feedback is always great.