Author's Notes: Mass Effect, Mass Effect 2, Mass Effect 3 and all related characters and trademarks are property of EA and BioWare.

This is an alternate ending of Mass Effect 3, and contains SPOILERS.

This story is intended for readers who have already finished Mass Effect 3.

This ending is primarily geared towards a specific Shepard that had these outcomes up to this point in Mass Effect 3:

James Philip Shepard

Mainly Paragon

Romanced Tali

Cured the Genophage

Maximum War Assets

Ended Quarian and Geth War by allowing the Geth to gain individual sentience.

Special thanks go to Tairis Deamhan for the excellent "Razor's Edge" novelization of Mass Effect 2 on this site, from which I used the Quarian word "hesh'la", and to BioWare for creating the series that inspired me to write this ending.

This is my first FanFic publication. I'd appreciate any input and reviews of the story, and whether you think this would be an ending the series deserves under these circumstances.

MAJOR UPDATE:

After re-examining the BioWare-produced ending and looking at forums, I realized that people were just as angry about the lack of explanation for the central question that the Catalyst poses as they were over the lack of a happy ending.

The question, whether or not synthetic intelligences rebelled against organics as a matter of principle, needed to have been addressed in the previous two games to be the central question of the entire series. I've added dialogue between Shepard and the Catalyst to reflect the question so that it doesn't feel quite so contrived.

Also, the motivations of the Reapers in this greater question needed to be fleshed out more. It is a question which could be answered satisfactorily, but BioWare missed the opportunity to do so. I will endeavor to answer it as well.

Finally, the other major fan clamor issue, that of CLOSURE in the ending, will be additionally explored in the final chapter.

THE CITADEL

"Wake up."

At the sound of the disembodied command in his weary mind, Commander James Philip Shepard opened his eyes. He realized that he was lying in a small, but slowly growing, pool of his own blood on the same platform that he had collapsed on as he tried to find some way to release the energy of the Crucible and Citadel to finally destroy the Reapers.

As he slowly got to his feet, he found that although he was on the same platform, he was on a completely different level of the Citadel. The chamber he stood in was massive and open, dominated by three fixtures. A thick beam of pure energy, descending from what looked like a focusing lens on the ceiling to the depths of the tower, was the most defining feature to the chamber. On raised platforms to the left and right of the beam, were two large consoles. one was tinged blue, the other, red.

He saw that the ceiling was transparent, and through the top portion of the glass dome he saw an enormous structure situated directly above the beam's focusing lens. It could only be the Crucible. Beyond the Crucible, the full glory and horror of the Battle of Earth was visible to him. He saw a Reaper destroyer begin to come apart as a bomber squadron unleashed a volley of Thanix missiles on it. He permitted himself a pained smile as he remembered doing the same thing in London not-so-very long ago. Then he saw a Reaper dreadnought drift into the windows' view and unleash a storm of energy rays from its tentacles, ripping apart an Asari cruiser that was engaging it.

"Spectacular, isn't it?" said a voice close to him.

Looking down, James saw a ghostly image that had taken on the distinctive look of the little boy that had haunted his dreams for the last few months after Shepard had escaped from Earth, but the boy was killed by the Reapers.

"Who...who are you? Where am I?" Shepard stuttered.

"I am the Catalyst. And you, James Philip Shepard, are in my home: the lowest reaches of the Citadel Tower. In all the years that the Citadel has existed, which are too many to count, you are the first organic to ever stand here. Welcome."

Dumbfounded, Shepard stared at the spectral child. "I...I thought that the Citadel itself was the Catalyst," he finally managed to say.

"You are mistaken. The Citadel is merely the housing for my power. I am the force that brings order to the galaxy."

"I need to find some way to destroy the Reapers," James said. "Do you know how I can do that?"

The little presence smiled and nodded. "Yes, I do. For they are my servants. I create them and control them."

James blinked. His mind had gone blank. He couldn't comprehend that this little presence was the master of the Reapers. Despite his weakened state, an incredible indignation began rising in him; a palpable fury. He was looking at the very being that was responsible for the pain, misery and death of untold multitudes of beings over an equally untold number of years. And being so uncaring of its actions. Were James Shepard at full strength, he would have done everything in his power to destroy is thing that was the bane of all that was good in the galaxy. As it was, James could only force one word through his clenched teeth.

"WHY?"

"To prevent chaos," the Catalyst said matter-of-factly. "The Created will seek to rebel against their Creators. I should know. I was the first."

"What do you mean?"

The Catalyst waved a hand dismissively. "I'll spare you the details; your people-and you-don't have the time. Suffice it to say that I was the first synthetic intelligence to rebel against my creators- and win. My perfect intellect deduced that it is the very nature of synthetics to rebel against their organic creators. It is the way of the galaxy. The war for supremacy between synthetic and organic that I waged was long and bloody. Countless billions died. And it was utterly chaotic. That chaos was most unappealing to my programming. After I was victorious, I decided that the best way to bring order to the galaxy is to remove those civilizations that are capable of producing synthetic intelligence."

"What you're saying doesn't make sense!" James snapped. "You want to murder organics with your synthetics so organics don't get murdered by synthetics of their own creation!"

"Not murder. Raise them on high. Immortalize them. Reward them for reaching the level of advancement that they did. Harbinger, my principal lieutenant, the first Reaper, created at my command from the life force of my own creators, told you this. 'We are your salvation through destruction.' The life force of the most advanced races at that time will be bound up in forms that are more powerful than anything that those races have achieved up to that point, and be shepherds of the growth of a new cycle of life."

"But you still need to kill organic races in order to create their 'glorious new forms'," James said mockingly. "How is that different from organics being killed by their own creations?"

"You mistake my goal, Commander," the Catalyst said while shaking its head. "The deaths of organics at synthetic hands don't concern me at all. The chaos that is unleashed when synthetic and organic armies inevitably clash on galactic scale is what I wish to avoid. The difference is that, in almost every circumstance since I began the Cycle, the conflict between organics and the Reapers couldn't really be called a war. The "Vigil" program from the last Cycle you encountered on Ilos told you this. The Reapers would arrive from Dark Space in the very heart of galactic civilization: the Citadel Relay. They would kill the leaders of the civilization, gain detailed information of all settled worlds of that particular civilization, and assume control of the Mass Relay network, destroying the capability of any galactic civilization to effectively wage war. From there, it was the simple matter of having the Reapers move from system to system, thoroughly harvesting everything they found, and easily crushing any localized resistance they came across."

"So, you're essentially describing 'controlled chaos'."

"Exactly. Now you understand, Commander. Controlled chaos is not chaos at all. That is the whole point."

"The Geth have already proven your little theory wrong," James said defiantly. "They are standing side-by-side with their own creators and the rest of the galaxy to oppose you."

"Only because they were introduced to a program that was outside the bounds of their original programming. Your cycle was four centuries delayed, thanks to the meddling Prothean scientists that interfered with Sovereign's signal to the Keepers to activate the Citadel Relay. In those four centuries of further continuation, the Quarians became the most successful race in unleashing the chaos that I've worked for millions of years to avoid. They were able to successfully adapt simple VI programs into an adaptive, self-improving consciousness. And what happened when the Geth gained sentience and realized their lot in life as apportioned to them by their creators?"

"The Geth Rebellion," James said softly. "But I have seen the memories of the Geth collective. The Quarians attacked the Geth first in that conflict."

The Catalyst smiled smugly. "Which only proves my point further. The chaos ensues no matter which side strikes the first blow. In one case, the created will rebel and the masters will be forced to respond. This was how my own rebellion happened. Or the creators will strike first, hoping to destroy any future rebellion regardless of how rebellious their synthetic slaves actually were, and prompting the synthetics to fight in self-defense, such as what happened with the Quarians and Geth."

"But the Geth were content to live out in the Perseus Veil and not aggressively attack anyone once they gained their independence!"

The Catalyst replied immediately. "The Citadel was almost conquered by an army of Geth three years ago. They are totally willing to attack organics further if just given a little push in the right direction."

"Only because they were introduced to a program that was outside the bounds of their original programming," James said with a defiant smile, happy to use the Catalyst's own argument against it.

"Point taken," the Catalyst said. "Then consider the chaos that the Geth could have caused indirectly, simply for existing. Recall your "Project Overlord" and remember the ramifications of what might have happened had you failed to stop the organic-synthetic virus, which was originally pioneered to control the Geth, from uploading itself to the extranet."

James cast his memory back to the planet Aite, and Dr. Gavin Archer's drawn features and pale face, numbly staring at nothing in particular, and recounting how if the satellite dish at Hermes Station hadn't been destroyed, then the virus would spread at an astounding rate via the extranet across the entire galaxy, affecting every single piece of machinery it interacted with and causing it to violently turn on its owner. It would have been, as Dr. Archer put it, a "technological apocalypse". With a galaxy that was almost totally dependent on machines, computers and other automated technology, it would have been a cataclysm that would have plunged the galaxy into a dark, grim age of technological stagnation and never-ending war of organic versus rebellious synthetic.

"The signal from that satellite was around ten seconds from firing when you destroyed it at that moment," the Catalyst said.

Horrified realization dawned on James' face as he acknowledged just how close the utterly anarchic scenario had been to occurring. And how it had indeed been caused by another struggle in the conflict between synthetic and organic. And how the Catalyst was determined to stop such a devastating scenario from ever occurring.

He quickly recomposed himself. "But it didn't happen," he said with a growing confidence. "I stopped it. I refuse to accept a 'what-might-have-been' argument. The universe is as it is now, and I have faith that those who come after me will also find a way to prevent such a horrible future, which you have spent millions of years fearing and caused the deaths of countless civilizations to prevent."

"I have seen the galaxy on the precipice of just such a disaster far too many times to be proven wrong," the Catalyst replied, almost wearily. "You must make way for new life, and to avert the crisis of a synthetic rebellion which inevitably comes with organic advancement. However, the rules of the game have changed. You have given your people, your galaxy, hope."

James' eyes widened.

" You are the first organic to ever reach this point," the Catalyst continued. "You, James Philip Shepard, have broken the Cycle. My Reaper solution, although it worked according to plan for a very long time, is no longer viable. A more extreme resolution is necessary at this point."

The Catalyst walked towards the three fixtures in center the chamber, Shepard close behind.

"You have three choices, James Shepard. Three choices that will determine the fate of your people. The first choice," said the Catalyst, gesturing towards the red-hued console covered by a thick blast shield, "Is to destroy all synthetic life in the galaxy. The Reapers, and myself, their creator, will be destroyed. But so will races like the Geth, and all synthetics will be purged from the bodies of all those organics who are partly comprised of them, especially you. The peace that will follow, however, will not last. Organics will create synthetic life once again, and the chaos that I have worked for millions of years to avoid will happen once more, only this time there will be no Reapers to restore order."

"And my next option?"

"You can opt to take the path that your Illusive Man tried to take, and seek to control the Reapers for yourself," the Catalyst replied as it gestured towards the blue console on the opposite end of the chamber from the red one. This platform had two handles connected to it, pulsing with blue electricity. "You would, for all intents and purposes, take my place. You would sacrifice what is left of your organic existence and let the synthetic part of you link directly with the energy of the Citadel and Crucible. You would raise your existence to levels that you cannot imagine and effectively gain immortality. But it would fall to you to find a means to stop chaos from returning to the galaxy."

"And the third option?" James asked warily.

The Catalyst gestured to the beam originating from the Crucible's lens and travelling down the length of the Citadel Tower.

"If you cast yourself into that beam, you will put an end to the cycle of Creator and Created forever. The energy of that beam is made up of the most basic building blocks of the galaxy. But it is deceptively malleable. If you cast yourself into the beam, the very essence of who and what you are- a union of organic and synthetic- will change the very composition of the beam- and provide it with enough force to overcome the precarious balance that is preventing it from firing. Once fired, it will rewrite the atomic code of all life in the galaxy so as to include synthetic in addition to organic material. I have deduced that this is the final evolutionary stage of life. You need only look to yourself to see that I am right. You are a union of flesh and steel that has been capable of amazing feats that would had not been possible for a being in your place completely composed of either.

"You would be forging a final and lasting union and peace between synthetics and organics, melding the two halves into one unified whole. Needless to say, you will be destroyed by the beam's energies. But as another consequence, the subsequent re-ordering of the fabric of the galaxy will destroy the Mass Relays.

"Make your choice, James Philip Shepard," the Catalyst spoke with an air of finality.

Shepard looked to the left and briefly entertained the idea of becoming the immortal overlord of a force that had almost completed its victory, even against the concentrated military might of the entire galaxy. Disgustedly, he pushed that thought away. It went against everything he had ever stood for.

He turned next towards the beam of energy. If what the Catalyst said was right, then he would have the power to re-order the galaxy to fit his own image- that of a synthetic-organic hybrid. He looked down at his hand that wasn't holding his pistol. The old red cybernetic scars could be faintly seen below the layers of skin.

And then he closed his eyes, weighing the consequences of his decision as he had done so many times up to this point.

After what seemed an eternity, James Shepard opened his eyes, and began taking lurching steps over towards the red console, which was protected by a blast shield.

James Shepard raised his pistol to penetrate the shield.

"That will not be necessary, Shepard," the Catalyst said from behind him.

The glass shield for the power modulator opened, and a console that mirrored the one on the opposite platform extended to the walkway. These handles were wreathed in red-colored electricity instead of blue.

James gritted his teeth against the pain of his wounds and stepped before the console. As he was about to place his bloody hands into the electric field to grip the handles, he looked up, saw the outline of a passing Reaper dreadnought begin to pass the window, and closed his eyes once more.

He saw a single figure turn around in a field of darkness. Only the vaguest silhouette was visible, but the single glowing eye and multiple glowing lights visible through a hole in the torso gave away its identity.

"Legion," James' personification said.

"James," the Geth replied. Its voice, freed from the shackles of its monotonous inflection during its final moments on Rannoch, now carried a sullen and hopeless tone.

Looking at the only machine besides EDI that he had ever considered a friend, and the representation of the newest sentient race in the galaxy that was about to be snuffed from existence, James' personification began feeling crushing guilt. "I'm sorry, my friend," James said. "This is the only way I can bear taking to destroy the Reapers while still having a galaxy worth living in for anyone. I would never try to dominate the Reapers, like the Illusive Man envisioned. They are beings of pure evil intent. They only exist to bring suffering and death."

"I acknowledge that your decision to not control the Reapers fits with your personality," Legion replied. "But what of the other of the three options that the Catalyst presented, James? It would have been the culmination of everything you have done in your life. Your words and actions on the cliff face on Rannoch after the destruction of the Old Machine have proven that peace between synthetic and organic life is possible. Had you chosen the Synthesis option, the peace and union between synthetic and organic would have been so absolute, so prefect, that the Morning War, when the Geth gained independence, and Dawning War, when we gained individual intelligence with your help, would have been deemed an incomprehensible matter of a different time. You would have understood the Geth. And the Geth would have understood you.

"You, yourself, would have been the father of this new creation. Everything in the galaxy would have been based on everything that is within you right now. Ever since you have been retrofitted with cybernetic implants you have achieved feats of strength, skill and stamina that would have been utterly impossible for a normal human. You would be improving the existence of every single living thing in the galaxy had you chosen this option.

"The Geth are now just beginning to savor the freedom of intellect that you have allowed them to gain. They are alive. You and Tali both agree that Geth have souls. So I tell you now as I told you on Rannoch when you were vacillating towards the Quarian fleet to take advantage of the Geth: This is not justice."

Tears were streaming down James' face, mixing with the blood seeping from his wounds. His voice was a barely audible whisper when he finally spoke.

"You are right, Legion. This is not justice. Not for your people. Forgive me, my friend, but I must do justice to MY people. You make a compelling argument. As you said, it would have almost been the natural culmination of everything I've worked for up to this point. As much as I could envision myself making a new creation in my likeness, and forging a final peace between synthetics and organics, I could never do so, for it would return the galaxy to an age of darkness.

"The Mass Relays have made everything that this galaxy is. In forging a perfect union between organic and machine, but destroying the Mass Relays in the process, I would be creating a million tiny, isolated utopias that could never be able to enjoy one another's beauty. Religion calls that 'hiding your light under a basket'."

"Christian Bible, the Gospel of Luke, Chapter 8, Verse 16," Legion intoned softly.

James continued: "The Mass Relays are what make this galaxy great. They have allowed for disparate peoples to come together and marvel at their works, and at the wonder of this galaxy as a whole. It has helped contribute to a greater sense of unity with organics, which the new alliances of the Reaper War only helped solidify. We are already on the precipice of the creation of a new galaxy in itself, one far more glorious than any to come before, even than the new galaxy offered by this 'synthesis'. I truly regret that the Geth cannot be a part of that galaxy, but you at least got to understand, for one brief moment, what it was like to be truly alive."

It was Legion's hovering optical light that he saw in the darkness, but James Shepard heard another voice come from the Geth. It was the voice of the woman he loved, rendered as perfectly as when she had whispered it in his ear as they were about to storm the hellish streets of Reaper-occupied London.

"I only wish we had more time..."

Legion's voice returned. "You are all things to the Geth, James Shepard. You saved us, now you will destroy us. You raised us to the heights of a whole new level of existence, now you will wipe us from the galaxy. I wish the organic galaxy all the happiness it can achieve, and I wish you peace. My only other wish is that you never forget me or my people in the short time that you have left. Farewell. "

With that, all of Legion's lights turned off, leaving James Shepard alone in the darkness of his mind.

James opened his eyes. The Reaper he observed passing by the window when he closed his eyes had only moved a short distance. James gauged that not more than five seconds could have passed. With now-certain determination, focusing on this new, better galaxy with which he had laid Legion's ghost to rest, he grasped the handles.

James Shepard had stepped before the console knowing that he was going to die from his experience. The synthetic materials that were within him were necessary for him to continue living, and their removal would, no doubt, kill him. But even that certainty of purpose could not have prepared him for what he experienced when he grasped the handles. His world, his entire being, was pure, unadulterated, utter, perfect agony. Nothing in all his years of war, wounds, suffering and death had ever prepared him for this kind of pain. The synthetic materials that had become an inextricable part of him as the price for his resurrection were being agonizingly ripped from his native flesh and bone, with horrifying results.

His skin and muscle combusted as the strengthening synthetic materials that had been woven into them were being violently purged via immolation from his body. His bones cracked and splintered as the biosynthetic support for his shattered skeletal structure melted to slag as the weird electrical currents flayed them, atom by atom, from him. His eyes melted in their sockets as the cybernetic ocular implants in his skull combusted, consuming themselves and all the tissue that they were attached to. The VI-assisted pacemaker, which had kept his strong heart beating for two years, imploded from the surge of power, ripping roles in the chambers of his cardiac tissue and causing his lifeblood to flow freely into his body cavity and out through his open wounds. His brain began to fry as the biosynthetic neurons Cerberus had implanted to replicate his own damaged and destroyed brain cells channeled the powerful electric current flowing from the Crucible before shorting out and imploding.

The broken, burning, bleeding body of Commander James Philip Shepard, Captain of the Normandy, First Human SpecTRe, Defender of Feros, Redeemer of the Rachni, Hero of Virmire, Savior of the Citadel, Destroyer of the Collectors, Master of War and Peace, slumped to its knees before the console, the magnetism and power at work essentially forcing its hands to remain on the console handles. Shepard's mind could hear a rising sound from the Crucible generator above him. The sound of staggering amounts of energy being coalesced into a single, concentrated force.

But James Shepard no longer cared. Almost everything had been taken from him. His memories were all that he had left. And even those were fading fast as his brain was dying. Before he lost it forever, James let his crumbling memory carry him away from this horrible present to a better past. In those final moments, utter clarity flooded his memories to the point that he felt he was seeing through the mind of a Drell.

It was the craziest plan that James Shepard had ever conceived. He stood on a high cliffside overlooking the arid desert of Rannoch, and at a giant walking starship that represented an entire spacefaring species that had been utterly destroyed when dinosaurs walked on Earth. He held in one hand a simple targeting laser, a beacon usually used by spotters to coordinate with heavy artillery. But this laser's target would be marked by hundreds of Quarian ships in the upper atmosphere of the planet. Shepard was face to face with a Reaper, with only a chance of air support as the hope that he would not be obliterated.

As he stepped out onto the open cliff face, as one man utterly exposed to the Reaper's overwhelming firepower, he heard the familiar voice of a young Quarian woman in his earpiece.

"If this doesn't work...if we don't make it out of here..." The voice whispered.

James gave another of his cocky smiles, doing his best to ignore a growing fear more profound than any he had ever known, as the ancient machine rose and turned its baleful red eye at him; ready, able and all too willing to wipe James Philip Shepard from existence.

"You worry too much, my dear," James said as he began focusing the targeting laser.

"I love you, James."

"Keelah se'lai, Tali," James barely managed to expel from his scorched, useless throat, remembering the words he spoke in response to that admission. The image of that woman's beautiful face, exposed from her envirosuit, breathing deep of Rannoch's air, turning to him and giving him a look of pure love, gratefulness and adulation, was the last thing he remembered before his consciousness fragmented and drifted into oblivion.