Hi everyone, this is the first chapter of a story that I am writing as an alternate version of Mass Effect 3. The plot of the original was full of Ex Machina elements like the Crucible and overly simplified resolutions to galactic conflicts that had lasted thousands of years. I intend to avoid these failures of creativity and make the finale to an excellent story as realistic to the universe as I can. I would like to think myself a fairly intelligent person, but as this is my first story here I welcome all comments, both criticizing and laudatory. One thing I will promise is that if people start to read my work, I will never go dark. Period. There is nothing I dislike more as a reader myself. With that done, let us be off.

Inside a Blue Suns Base

Shepard ducked beneath the nearest piece of cover, ejected a red hot thermal clip, and shouted into his comm unit, "Garrus, flank the right side. I'll draw their fire". Without waiting for a response, the Commander jammed in a fresh heat sink, jumped over the waste high crate he'd been crouching behind and into the line of fire. He threw up a biotic barrier between the mercenaries and himself, sprinted to the left side of the base. The Suns' fire immediately swung in his direction, trailing after him and loudly impacting the base's steel wall. If it weren't for the cybernetic implants that Cerberus had used to turn him into a super soldier, he never would have been fast enough to keep out of the line of fire, even if the mercenaries could not shoot for their lives.

Fortunately for the Commander, he only had to run a short distance. Garrus had fought plenty of battles both with Shepard and against the Suns. The mercenaries' fire quieted as quickly as it had begun when Garrus slipped from his position of cover, just after Shepard, and ducked around the side of the room. He easily rolled a grenade behind their lines and watched as they realized what had happened…an instant before being blasted in five different directions by the supercharged inferno grenade.

After checking to see that the mercenaries were, in fact, dead, which the large amount of gore filling the base confirmed, Garrus pulled his helmet off and chuckled, "Jeez Shepard, you would think you would get tired of my saving your life, that has to be the third time this week."

"You're welcome. Without me drawing their fire your ugly mug might have picked up a couple extra scars. It's called teamwork Archangel, no 'I' in team."

"That's where you're wrong Shepard, there totally is in Turian. Way to go all human-centric on me."

Shepard laughed and looked his friend over, the former C-Sec officer had been with him through thick and thin. In just over two years he had taken down Saren by his side, watched Shepard die when the original Normandy was destroyed, and stormed through the Collector base on a suicide mission. Although he had replaced his pitted and scarred blue armor after their trip through the Omega 4 relay, the scars covering one side of his face betrayed the battles he had followed his Commander into.

The Spectre knew that even if nothing else did, his friend's scars would always remind him of the struggle he had in keeping his team safe. He knew there was little he could have done to protect Garrus from the rocket that had left him in the med bay for weeks, but he nonetheless was left with a feeling of guilt. It his life's mission and death that drove his friends to their pursuits after the destruction of the SR1. Garrus' mission, becoming the vigilante Archangel, had dramatically changed his friend. It cost the Turian friends, his health, and the optimistic view of the universe he had been struggling to hold onto during the fight against Saren. Garrus was a darker person that he had been, and that was on Shepard.

The SR2 Normandy - Shepard

Shepard stumbled into his cabin half drunk and wondering what to do next. Not literally then and there, but over the next month and year. His thoughts were only half put together and blurry from the booze, but he remained coherent enough to know that he was acting without the drive that had carried him through his fight against Saren and mission to take down the Collectors. The Commander felt as if he was bashing his head against the wall of his room for the last few weeks. It had been nearly a month since his solo mission to Aratoht to delay the Reapers, and since then the Normandy and her crew had only been running errands for Admiral Hackett. His team was getting angsty and beginning to suspect he didn't have a further plan. Shepard knew that the Reapers were on their way and that he probably, at best, only had a year before they arrived. He just wasn't sure what to do next. To his knowledge the Reapers didn't have any other vanguards awaiting their arrival and he had no idea where to even begin looking. There just wasn't anyone for the Normandy and its crew to fly off to and kill.

He climbed into his bed still stinking of the cheap beer he had shared with the ground team in the cargo bay after they had cleared the Blue Suns' base and seized the small Prothean artifact that they'd stolen. That was what his team had been reduced to, anti-piracy measures and protecting antiquities from generic thugs. The Normandy would be briefly meeting up with the Fifth fleet to deliver the bounty of the last month before heading back out to search for more Prothean tech. Hackett had claimed the ancient technology they gathered could be a game changer, but Shepard knew it could only do so much. They could gather all the Prothean records remaining in the galaxy, but information from a race that had lost their own fight against the Reapers couldn't save them.

It wasn't like they hadn't been productive after the Suicide Mission either, They put down the rogue Cerberus AI project on Aite and prevent a Cerberus take over of the Geth in the process. Shepard, Liara, and Thane had killed a rogue spectre and installed Liara as the Shadow Broker, making an ally of one of the most powerful individuals in the galaxy. And on Aratoht Shepard had blunted the Reaper's arrival, delaying their attack on the galaxy.

Hackett had sent him on that mission and Shepard was sure that it was only the Admiral's effort to keep the mission off the books that kept him from being dragged back to Earth for a court martial. The Commander didn't regret his actions, but he felt an unmeasurable burden on his conscience. It was the same ache that plagued him after he chose Ashley on Virmire. If nothing else was, Aratoht was the ultimate testament to how far he was willing to go to stop the Reapers.

After Aratoht however…there had been nothing. It was like the fights just stopped coming and he was left wandering around aimlessly on near pointless missions. What did those lives he took destroying the relay in the Bahak system matter if he wasn't going to keep fighting to stop the Reapers? He wanted to fight, he was aching for it. The Reapers just weren't giving him one.

Shepard fell asleep reliving the nightmare of his death at the hands of the Collectors. Watching his ship and friends murdered around him, fighting to the end to save each one, and being ejected into space. He was left floating there as the air that sustained him slowly emptied itself from his suit.

EDI's voice carried her wake up call across his cabin, "Commander, we will be rendezvousing with Admiral Hackett and the Fifth Fleet in just over an hour. You have been asleep for eight hours and 43 minutes."

Shepard couldn't remember the last time he slept for so long, it was a nice change. He stood up, stretched, and made his way over to his bathroom. Having his own shower had to be the nicest addition to the SR2. "Thank you EDI, let the crew know I'll be right down."

"Of course Commander, signing you off"

Shepard hurried through his morning routine of showering, brushing his teeth, and shaving before heading out of his cabin. He waited in the vestibule between the elevator and his cabin for the galaxy's slowest elevator to finally open for him. The Commander had to dodge out of Kelly's way when she stepped through the open doors staring down and not noticing him waiting there. She'd been distracted by the old-fashioned clipboard she was carrying and hadn't noticed him.

"Kelly, what can I do for you?"

She glanced up in surprise and took a moment to recover her composure. When she spoke it was without her usual chipper tone, "Well Commander, some of the crew and I were a little concerned about meeting up with the Alliance. We're technically part of a terrorist group since…we're all still officially Cerberus."

Shepard rubbed his face as he realized their rendezvous with the Fifth Fleet would be his first time aboard an Alliance ship since the original Normandy's destruction two and a half years earlier. Seeing Kelly's worried expression, he smiled and did his best to comfort her, "Tell everyone there's no need to worry. I'm working on full pardons for the entire crew, and I will make it happen. The risk you took when no others were willing won't be forgotten." Shepard hit the button for the 2nd deck and the elevator began its agonizingly slow descent.

Kelly nodded, "Thank you Commander, we knew you wouldn't forget about us. Just…after what the Collectors did no one wants to spend any more time in a cell."

Shepard pulled Kelly into a hug. Watching the colonists liquified in front of his eyes and fearing for his crew was one of the most painful experiences of his life. "I promise that I'm taking care of it, I'll find a way."

—-

He stood on the platform in the CIC overlooking the star map. It was a relic of the Turian contribution to the SR1. The Commanding officer was supposed to look down upon the CIC. Shepard knew it had something to do with promoting the chain of command and making orders seem more important. He liked it because the view was unlike anything else. From the platform one literally looked down upon the galaxy and chose where to travel to. There was a unique sense of control over one's destiny when they held that power.

Shepard had already checked his messages, scrolling through dozens of thank you notes and hundreds of requests for his help. He did his best to help where he could, taking down pirates and plundering mercenaries. At the end of the day though, those were side missions. The requests were minor compared to the threat looming over the galaxy and every person in it.

He glanced around the CIC, full of his crew, before deciding to step down from the platform and head into the lab to speak with Mordin. The scientist possessed the most eccentric and brilliant mind Shepard had ever encountered. Mordin was the mad scientist with a plan for every conceivable contingency, no matter how outlandish. If there was anyone in the galaxy equipped to figure out ways to fight the Reapers, it was the Salarian that created a cure for a plague on Omega, created a Seeker countermeasure in just a few days, and reshaped the galactic balance of power by genetically modifying an entire species.

Moments later the Commander stepped into the Normandy's lab. Mordin looked up quickly, "Ah, Shepard, good to see you, had request to make. But why are you here?" The Salarian paused for a brief moment and raised his hand to his chin, giving him a thoughtful appearance. "Not related to delivery of tech to Admiral Hackett, already told you what we found. Unlikely related to existing Collector research without external stimuli to induce your trip here. You did not take advice on risks of biological contact with other species prior to mission. Best just to ask. What do you need?" Mordin returned to working on whatever experiment he had in front of him.

"I don't know that I've ever stumped you before Mordin."

"Not stumped, stumped would imply that I had relevant data to support a hypothesis. I do not."

"I'm here to ask for your advice Mordin." Mordin nodded, seemingly suggesting he had at least some idea of what Shepard had come for, even if he had not initially claimed to.

"Last time I gave advice, was ignored. You took few of the precautions suggested when" Shepard interrupted.

"I know Mordin, I regret that. That advice was unsolicited though. I'm asking for your help this time."

"Must admit, intrigued. What's troubling you Shepard?"

"I don't know what I'm trying to do right now. I was thrust into saving the galaxy from Saren and the Collectors. What comes next?"

Mordin never looked up from the table in front of him, "Not surprising you have trouble finding new missions. Every time you made a name for self you were reacting: fighting Batarians on Elysium, stopping Saren after Eden Prime, moving against the Collectors after kidnappings. Never proactive, only reactive. Be proactive"

"I think that's an oversimplification Mordin. I haven't exactly had time to figure out what do do next to this point. Waking up from death kind of put me at the mercy of the situation, forced me to work with Cerberus."

"True, but you have time now. Now don't know what to do."

The Commander shifted uncomfortably, he was losing this debate, even in his mind. "So be proactive huh? That's helpful."

The Salarian finally looked up from the table in front of him and set down the beaker and pipette he had been holding. "Everything you've done is to fight the Reapers yes?" Shepard nodded. "Perhaps consider not fighting them now."

"Mordin, I don't follow."

"The Collectors, Saren, Geth Heretics, all agents of the Reapers. All stopped. The threat persists. Stop and wonder what happens when they arrive."

Shepard shook his head, "The Council hasn't listened so far, I'm not confident in their ability to change their minds."

"Then don't try. Make galaxy stronger to fight threat, this is not all your war. Entire Galaxy's."

Shepard was about to interrupt and disagree, but stopped. Mordin was right. He could fight the Reaper's pawns all he wanted, but they were all going to die when the Reapers arrived. He needed to change that calculus, give them a chance. "Mordin, the Krogan…"

Mordin looked at the ground for a moment. Turning around to face the darkness of space behind him he slowly nodded, "Thought about this, was favor I wanted to ask you. I desire resources and facilities to modify genohage again, reduce birthrate to manageable level without the miscarriages." He shuddered, "Miscarriages terrible psychological weapon. Should not have been forced onto Krogan. Ever. You have necessary connections to Krogan, and resources to fund effort. Have some in savings myself, not enough for task."

"I thought about it before we went through the Omega 4 relay. Wrex was a good leader, but I wasn't sure they were ready for a cure. He needed time to unite his people, stomp out rebellious elements." Mordin kept his eyes on Shepard but made no comment. "That was what I thought, but we're out of time. We need their help. We'll find a way to get you and the equipment you need to Tuchanka to begin your work, and I'll talk to Hackett and the Council."

"Thank you Shepard, and thank you for keeping Maelon's data. Will be invaluable. Also, before mission, knew Council must be convinced of Reapers. Gathered evidence." Mordin sent Shepard a package of data over his omnitool. "Give this to the Council. Should be enough."

"For some reason I find that hard to believe."

"Will be. Easy to dismiss theory or hypothesis, even with some data to support, when conclusion is grim. What's the human phrase?" Mordin paused, "Ah yes, seeing is believing. Footage of collectors, Reaper, scanning data of Collector base, and DNA samples comparing Collectors to Protheans hard to dismiss. Especially if you threaten to release data released to public."

"I hope so, but even if they acknowledge there's a threat, something tells me convincing them to change their minds on the genophage still won't be easy. Thank you Mordin, after this meeting with Hackett and the Fifth Fleet we'll head to the Citadel to buy equipment and speak to the Council. If they agree we'll head to Tuchanka and set you up immediately, money could be an issue but we'll find a way." Shepard turned and walked out of the lab feeling better than he had in weeks. He would face the Council for the first time in months, prove the Reaper threat, and start unifying the forces he would need at his back when the Reapers arrived. First the Krogan, then the Quarians, and if the council started building up military forces they might have a chance. A slim one if they couldn't gain some other advantage, but a chance nonetheless.

Shepard smiled. He had a mission, and this time it wasn't one thrust upon him. He was taking the offense.

I edited this chapter a few times after its original posting. It now contains a bit more exposition and background and hopefully better represents the story's quality. (TGJE - 4.26.2016)

As a side-note, the quality probably dips a bit after this chapter since I rewrote it without rewriting the next few. It will get better as the chapters go by.