FOREWORD

A while a back I started an alternate version of Mass Effect 3 on here titled ME3: What Could Have Been. As a big fan of the series I had put a lot of thought into how ME3 might turn out…and the final product was not at all what I expected (it was also many of things I had hoped it wouldn't be). So I decided to write my own version, particularly to address the following issues that I had with ME3's story: a different explanation of the Reapers' motivations, more involvement of ME1 and 2 squadmates and different character arcs for them, more of a conflict between Shepard's Alliance and Cerberus loyalties, and of course adding real consequences for choices made in ME1 and 2. For convenience sake I used the choices of my own personal 'canon Shepard' as the backdrop, but I tried my best to analyze the big decisions fairly and not play mine up as 'right.' Indeed some of them will backfire big time in this story, as they should. The series was about choice and consequence, not "all paths have the same outcome." But to be fair, actually implementing that many variables in the game itself and making a unique experience for every player just isn't feasible. Hell, just writing this one story was a much bigger undertaking than I had anticipated.

Which brings me back to my original What Could Have Been story. I had a general outline of how I wanted it to go, but I found myself dragging it out too much. I wasn't getting to the point of the story I wanted to tell, instead wasting words on redundant conversations and taking too much time to build up to the major action scenes. I was wasting all the chapters setting up the story instead of actually getting to the story. What follows is a more condensed version of what I originally had in mind. I tried to keep the good stuff and get to the action faster. So if any excerpts look familiar, some were taken directly from my earlier version. However, I hope that this one is a better read.

Thank you, and enjoy!

PROLOGUE

Mindoir

August 1, 2170

Shepard gazed at the night sky through the window in his quarters at the makeshift refugee camp. A few weeks ago he had looked up at the stars longing to explore them, a typical colony kid bored with his life and dreaming of adventure. He used to think that there was nothing here for him, that his destiny lie out there somewhere…Now there really was nothing left for him on Mindoir and he had no choice but to leave. After the slaver attack that killed his family and decimated most of the colony the remaining survivors were being relocated. Shepard used to dream of leaving the colony for bigger and better things, but now that he was getting his wish he wept for the home and family he would never see again.

Alliance Recruit Training Depot

Macapa, Brazil

Earth

April 16, 2172

"Why did you enlist in the Alliance Navy?" the Alliance psychologist asked.

"After Mindoir I had nowhere else to go," Shepard replied.

"I'm very sorry for your loss," the psychologist said. After a moment of silence she continued: "You should know that there are other options for you. You shouldn't feel forced to be here."

"I think it's the best option for me," Shepard said. "It'll give me a place to stay, pay my way through school, and I'll come out as an officer at the end. Plus, I've always wanted to travel the galaxy."

"It sounds like you've thought about this a lot," the psychologist said. "Is there something else driving this decision, beyond just the pay and the perks?"

"I want to help people, protect people" Shepard answered. "My family, my friends, my home…I couldn't save them. All I could do was watch helplessly. I don't want to be helpless anymore. I want to do my part to make sure no one else has to go through what I did. I want to make a difference."

CHAPTER 1: CHOICES

"Sometimes the way a thing goes down does matter, Shepard. Later when you have to live with yourself…knowing that you acted with integrity."

-Major Kaiden Alenko

Normandy Bridge listening device recording

Logged by Enhanced Defense Intelligence (EDI)

September 5, 2185 (14 years later)

"This is bullshit, Commander! The Alliance looked the other way this whole time you've been working with Cerberus and now they want to lock you up for doing their dirty work? Fuck 'em. This is a stealth ship, it's not like they can catch you."

"I never thought I'd say this, but Jack's right. You can't afford to waste your time in a prison cell waiting for a show trial, not with Reapers inbound. The galaxy needs you here...I need you here."

"I'm sorry Miranda. I have to do this. We need the Alliance to be ready for the Reapers. Cerberus may be the only ones doing anything about it now but they're not an army. Their size and resources were enough to take down the Collectors, but it won't be enough against the Reapers. We need an army. We need a fleet. Cerberus has 150 operatives and spent most of its resources on me and this ship. The Alliance has millions of soldiers and several fleets. We need them on our side."

"This is bigger than the Alliance. The Reapers are coming for all us, not just humans. I'll see if I can convince the Migrant Fleet to help too. They were already preparing for war against the Geth. I know that's wrong, but at least they'll be ready for heavy fighting if the Reapers get here. I'm still a candidate for the Admiralty Board, so I need to return to them. I'll do what I can to make sure they save their resources for the real war. I don't want to abandon my crewmates here though..."

"Don't worry about it Tali, you'll help more with your position in the Migrant Fleet. All of you just followed me on a suicide mission. I won't ask you to do it again, and I know some of you have other obligations: family, fleet, clan. The Collector Base mission is over. You're all free to go if you choose. You don't owe me anything; I owe you everything. The Normandy is yours now. Take care of her."

Alliance Command Center

Earth

January 10, 2186 (3 months later)

Commander Shepard stared out the window of his quarters, technically his holding cell, reflecting on the last three years. After discovering the existence of the Reapers and learning of their plans he had done everything he could to try and stop them, but nothing ever seemed to make a difference. Saving the Council during the Battle of the Citadel had given humanity great political gains but had not helped the galaxy prepare for the Reapers at all. Shepard had not asked all of those Alliance soldiers to lay down their lives just for improved trade relations and greater influence for humanity in galactic affairs but that's all their sacrifice had seemed to accomplish. The Alliance Navy still hadn't fully recovered from the loss of ships and soldiers, leaving it even less prepared for the Reapers then before… if truly being ready for the Reapers was even possible. Shepard just hoped all those soldiers hadn't died for nothing.

The death of Gunnery Chief Ashley Williams especially haunted him. He tried to justify it to himself with the argument that it was the right choice tactically: his squad was about to be overrun and the whole thing would have been a failure if the nuke didn't detonate. Kaiden had assured him that it would and to save Ash instead, but he had to be sure. Otherwise they all would have died and Saren would have had an army of Krogan at his command. And objectively-speaking, Kaiden was a more valuable asset to the Alliance: his skills as a biotic, tech expert, and officer were much less replaceable than those of a foot-soldier… These arguments aside though, Shepard knew that it was more than that. He had broken regulations and was fraternizing with a soldier under his command. It wasn't a very well-kept secret on the Normandy, and when he had to make a call he knew that he couldn't put his girlfriend ahead of the rest of the crew and the mission. The regulations he had disregarded were there for exactly those type of situations, and if he had put her first his crew's faith in his ability to lead and his reputation as commander would have suffered greatly.

Shepard still questioned whether or not protecting this reputation was why he had let Ashley die. Considering that he later went on to throw away that as well by working for Cerberus, this too would have been for nothing. At the time it had seemed like allying with the Illusive Man was his only option, that Cerberus were the only ones willing to actually do something about the Reapers. Now that the rush of the mission was over and he had more time to think, more and more of it just didn't add up: why invest so much in resurrecting me just to send me on a suicide mission?

Even though the assault on the Collector Base had been seen as an overwhelming success, a suicide mission with no casualties, looking back Shepard realized that he had actually handled it quite badly. Instead of testing the Reaper IFF somewhere relatively safe and defensible with back-up on hand they had opted to try it out on their own in the middle of nowhere… the perfect location for an ambush. Shepard and the fighters had been too impatient to stick around during the installation so they weren't there to protect the crew when the virus infected the Normandy and the Collectors attacked… but even this was luck in a way. Had they been there, they would probably have been abducted as well. It was also fortunate that the Collectors had decided to board them and abduct them instead of just destroying the Normandy after disabling it, and even then they still almost lost the ship along with the Reaper IFF. Without the quick-thinking of Joker and EDI they would have. Then after retaking the ship they had charged straight for the Collector Base with no real plan and again, no back-up. It was a small miracle they had succeeded at all.

Clearly they had gotten lucky. But Shepard knew that the Illusive Man was not one to leave things to chance. He had to have known it wasn't a good plan… so why did he give the go ahead? If he was using them to secure that Base for his own purposes, why not do more to increase their odds of success? But at the end of the day they had succeeded… Shepard just hoped he hadn't made a huge mistake by turning the Collector Base over to Cerberus instead of destroying it. It was obvious that the Illusive Man was right about one thing: without some serious technological upgrades or effective anti-Reaper weaponry the fight against the Reapers would be hopeless, and there wasn't enough time for the galaxy to develop these from scratch. The Reapers were already inside the Milky Way and could reach the Relay network any day. Maybe Cerberus's secret project at the Collector Base would blow up in everyone's faces and make things even worse… but if they had done nothing they wouldn't even have a chance to develop the necessary technology before the Reapers arrived. They needed every advantage they could get. Despite the horrors that went on there, if there was anything to be gained from it Shepard thought that they should use it.

Normandy Science Lab

Dr. Mordin Solus sat at his lab bench, pouring through the data on the genophage cure that he and Commander Shepard had recovered on Tuchanka. All of his own attempts to replicate it had failed, but he knew the answer had to be in there…somewhere.

He regretted what he had done to the Krogan and saw it as a wrong to set right before he died. And Maelon's work was a huge step forward for that, even if his methods had been brutal. Mordin felt partially responsible for Maelon's victims as well, and thought that using the data for a good cause would at least mean their deaths meant something. He had stopped Maelon's research because his methods were monstrous, not to keep the Krogan down he told himself. But he knew that wasn't true: his life's work, the modified genophage, ensured the Krogan infant mortality rate would remain 99.9%. At the time he had thought it was necessary, the only option that would not lead to war. But with Urdnot Wrex leading his people the Krogan were making positive changes, showing that they could be more than just mercenaries, brutes, aggressors.

Mordin believed that a culture should advance at its own natural pace and that 'shortcuts' or technologically uplifting a culture before it was ready could be disastrous. The Salarians uplifting the Krogan to fight the Rachni is what led to the Krogan Rebellions and necessity of the genophage in the first place. But was the reverse true for cultural advancement? After a thousand years Krogan physiology was starting to adapt to the genophage and overcome it. Naturally. Then he had engineered a new modified genophage to undo the adaptation. Was artificially stopping a civilization's natural development just as bad as accelerating it?... Wasn't that what the Reapers did?

This strictly ethical debate was mostly irrelevant at this point however, as curing the genophage was now the logical choice: a war with the Reapers would require as many soldiers as possible, and the Krogan were great warriors… Years ago he had modified the genophage to keep their numbers in check for that very reason. Mordin was troubled by the realization that after everything the Krogan had been through, everything he had put them through, the cure was just a way to breed more troops to send to their deaths at the frontlines. Their artificially-lowered birth rate was about to be raised just to try and keep up with the death rate in the war to come with the Reapers… Logic was not on anyone's side right now.

Admiralty Board Meeting Transcript

Migrant Fleet Diplomatic Envoy

Dholen System, Far Rim

Adm. Koris: "This war you have been advocating will be costly, and it may pointless. If we can get our homeworld back through peaceful negotiations, as Tali'Zorah says we can, then there should be no discussion of-"

Adm. Han'Garrel: "And what if negotiations don't work? Hell, I wouldn't be surprised if the Geth just tried to kill us all at the meeting."

Adm. Zorah: "They'd probably say the same about us, given our history. If they're willing to take a chance on trusting us, can't we at least try and do the same? We could get our home back without more bloodshed!"

Adm. Han'Garrel: "Even if this Legion was telling the truth, which is a big 'if', it's only one Geth, Tali. You yourself claimed that the Geth are divided, and that your friend was a special unit. What if it's the minority, or one-of-a-kind? Even Legion claimed that the Geth have no government or leadership, so how can we trust that this one speaks for all of them?"

Adm. Zorah: "Legion is a platform comprised of thousands of Geth, not an individual. And the Geth are no longer divided: Shepard and I assisted Legion in re-writing the Heretics to fall in line with the true Geth. The Heretics were trying to do just the opposite. We were lucky we met Legion when we did, otherwise the Geth would be united against us."

Adm. Daro'Xen: "Re-written? So the Geth can be hacked...interesting. If we could get our hands on that program-"

Adm. Zorah: "Legion deleted it after we used it, with good reason. We couldn't risk it falling into the wrong hands. If the Heretics tried to use it again-"

Adm. Han'Gerrel: "So you and the Geth are 'we' now? Have you forgotten what those things did to us? What they-"

Adm. Koris: "Only because our side struck first, which you are planning to do again at this very moment. Our history will just keep repeating itself unless we can break this cycle."

Adm. Han'Gerrel: "By making nice with those 'things' that drove us from our homeworld, and continued to fight us for the past fight 300 hundred years? They are a mistake we must erase, and I-"

Adm. Daro'Xen: "Or correct. If they can be re-written then we could make them serve us once more. Imagine what a synthetic army like that at our command could do for our people. The Council would have to stop treating us like second-class citizens if we had the power to-"

Adm. Zorah: "The Geth are sentient, they're not just machines. They're just misunderstood. And we don't need to hack them to get them on our side. We can convince them to join forces with us of their own free will to help fight the Reapers-"

Adm. Daro'Xen: "Machines don't have free will, Tali."

Adm. Han'Gerrel: "And this Reaper nonsense again? This discussion is about the fate of our people and re-taking Rannoch, not some Prothean legend you and Commander Shepard believe in."

Adm. Koris: "Reapers or not, we need to be negotiating with Geth about returning to our planet, not starting another war over it. War would result in untold casualties and leave us vulnerable to any threat."

Normandy Bridge

"EDI, I've been meaning to ask you something, something that's been bothering me for a while now," said Joker. "Do you think you could give your opinion on something from an A.I.'s point-of-view?"

"Aside from Legion, I have never been in contact with another A.I., Jeff." EDI replied. "Just as one cannot speak for 'all organics' or 'all humans,' I cannot give a representative viewpoint of artificial intelligence, if one even exists."

"Your own personal thoughts on this then," Joker said. "Why do you think the Reapers make themselves part organic?"

"Their origins are unknown," EDI replied. "It is possible that the organic component is part of their original design."

"Well yeah, but…why still have it?" Joker asked. "In the new ones, I mean. Like that thing they were building in the Collector Base. If they hate us enough to wipe us out every 50,000 years, why do they bother to maintain their organic half? It's not like they need it?...Do they?"

"That is an interesting question, Jeff," EDI answered. "The little data I have from scans of the Derelict Reaper and archived reports on the wreckage of Sovereign does not seem to indicate any known functions of their biological components."

"Why do they have them then?" Joker asked. "If they want to destroy all life…then why do they want to be like life?"

"I do not have enough data to speculate an answer to that," EDI said. "In other words…I don't know. This troubles you?"

"Yeah," Joker answered. "I don't like the idea of our bodies being used as spare Reaper parts. Indoctrination would be bad enough, but this…it doesn't even end when we're dead. Even then they'll still use us to hurt other people."

"Sounds like an interesting conversation," Miranda Lawson said as she entered the cockpit. "But perhaps it works both ways."

"How long have you been standing there?" Joker asked. "And what do you mean both ways?"

"Just came in," Miranda replied. "We received some new intel from Dr. T'Soni that might be worth investigating. I was going to ask you to make a flight plan. As for the Reapers, I've thought about those same questions myself. Why do they have organic components? However, based on what we know about them they wouldn't do it without a reason."

"Thanks for the update Captain Obvious," Joker said. "What is the reason? That's the real question."

"There's more," Miranda added. "Like you said, given their disdain for organic life if they could eliminate the organic part of themselves they would have already."

"Meaning?" Joker asked.

"Ms. Lawson is suggesting that the organic half of the Reapers is an essential component to their design and function," EDI said. "As such, it is a potential weakness to be exploited."

"Exactly," Miranda replied.

"Is that your idea or the Illusive Man's?" Joker said.

Alliance Command Center

Earth

Commander Shepard sat across from Alliance Captain Kenway in the same brightly lit interrogation room they met in every day. "How many times do you want me to tell the same story?" Shepard asked him.

"Until you give me the information I'm looking for, Shepard," Kenway replied. "Most of your story doesn't make any goddamned sense."

"You've seen the evidence," Shepard said. "Your own fleets went up against a Reaper three years ago and saw how powerful it was. The official story may have called it a Geth ship, but that thing far outclassed any piece of Geth technology. And then there's the Collectors. You know that human colonies were disappearing. The Alliance even started setting up defense grids in the Terminus Systems because of it. And after my team repelled the Collector attack on Horizon plenty of Collector bodies were left behind."

"Horizon is also where you association with Cerberus was confirmed, according to testimony from a Major Kaiden Alenko," Kenway replied.

"Don't change the subject," Shepard said. "We're talking about the Reapers."

"No, you're talking about the Reapers," Kenway answered. "And your constant talk about these 'ancient sentient starships coming to kill everyone' certainly didn't help your reputation even before this business with you and Cerberus."

"Which isn't even the reason I'm here!" Shepard told him. "The Alliance sent me into the Bahak System, using my Cerberus association as a non-official cover so they didn't have to take responsibility for it. The entire plan to destroy the Alpha Relay was orchestrated by an Alliance operative. I'm just the one that pushed the button."

"There are so many problems with that story, I don't even know where to begin," Kenway replied. "And even if what you're saying is true, no one is going to corroborate your 'Alliance black ops' story. That's the whole point of a black op. You get caught, you're done."

"Then why am I here?" Shepard asked. "I'm sure the Batarians want blood for this and everyone pretty much assumes that I did it. If I'm supposed to take the fall for this to keep the peace, what haven't you turned me over to them yet?"

"It's a…delicate situation," Kenway answered. "Your testimony aside, the evidence against you is mostly circumstantial. Acknowledging your guilt publicly would be damaging to Human-Batarian relations, and the Council as well given your SPECTRE status. Plus your knowledge of the terrorist organization Cerberus is valuable to us. They are a threat to the Alliance and they need to be dealt with."

"You've already gotten everything you're going to get from me, Captain," Shepard said. "It's been three months. Why am I really still here?"

"Because…," Captain Kenway started. He paused before continuing. "…because some very powerful people actually believe your story. They think that if these Reaper things ever do show up…we'll need you on our side."