The last thing Shepard remembered, she was trying to rescue Joker from the Normandy SR-1. The Alliance flagship, the best in the fleet, had somehow managed to get destroyed in a single, surprise attack. It was just another routine mission, and it ended with Shepard gasping for air, then succumbing to the darkness. The Geth had not stopped her. Saren had not defeated her. The Reaper, Sovereign, could not prevail against her. But now, she was taken by a damaged space suit.
Murmurs, and then explosions and sirens. A strange voice called to her, beckoning her into action. As if Shepard had never left the battle on the Citadel, she jumped into the fray around her, hardly even noticing that her biotics seemed more precise and her aim almost effortless. Hardly noticing the Cerberus logos stamped on the walls of the facility where, apparently, mechs had gone haywire. All she could grasp was that she was alive, she had a gun, and someone needed her help.
"Shepard, you're alive!" said another unfamiliar voice. He called her over, introducing himself as Jacob, a former officer in the Alliance Navy. He shot a biotic blast toward some enemy mechs. "If Miranda has you up and running, things must be real bad."
"Miranda? What the hell is going on, and where am I?" Shepard thought the name sounded familiar, but couldn't place it. She popped out of cover and buried some bullets into the heads of two mechs across the room. When she dropped back down, Jacob checked to see that the coast was clear.
"Nice shooting, Commander. Good to know you haven't lost your edge. I know you've got questions, but things are bad here. We've gotta find Miranda and get the hell out of Dodge. We'll fill you in once we're safe, deal?"
Shepard nodded, "If that means you're going to help me stay alive, we have a deal."
They made it through a few rooms and found a stray scientist, and they managed to take down some security mechs with a biotic warp field. Shepard didn't even have time to analyze what was happening around her. Defense and survival were her highest priorities, and soon enough they found Miranda, who promptly shot their scientist companion.
"What the hell," Shepard exclaimed, pulling her gun up squarely at Miranda.
Jacob, clearly startled, put his hand on Shepard's gun. "Wait, Shepard, it's alright."
"Alright?! She just gunned down an innocent man!"
Miranda chimed in, and Shepard recognized her voice from the comms, the one who was telling her where to go and what to do. "Hardly innocent. He's the one who set the mechs on us."
Shepard hesitated, then slowly lowered her gun. Nothing about this served to abate her confusion. The strangers around her seemed like they knew her well enough, though Shepard didn't particularly feel like this "Miranda" liked her at all.
"Is someone going to fill me in, now that we've dealt with the pyrotechnics?"
"Let's get in the shuttle first," Miranda insisted, not waiting for them to follow before boarding.
"Shepard," Jacob started uneasily after they strapped in. "You've been dead for two years. Miranda here has been leading the team of scientists that rebuilt you." Jacob was a strong soldier, with powerful biotics. He seemed trustworthy. But the news he delivered seemed unreal. Shepard took a few long moments analyzing his face and Miranda's for some sign that they were joking. Failing that, she swallowed the lump which had been forming in her throat, her brows knit together.
"Shepard," Jacob continued, glancing at Miranda, "If I tell you who we work for, will you still trust us?"
"Jacob, I don't think-" Miranda started.
"She's going to find out sooner or later. She needs to know."
Shepard straightened in her seat and let out the breath she had been subconsciously holding. "What is it? I mean, you just told me I died and got resurrected. Are you sure you can still surprise me?" Her hands were held out in surrender.
Miranda sighed, continuing in her Aussie accent, "What Jacob's heart of gold is trying to say, Shepard, is that Cerberus rebuilt you. I was in charge of the team of scientists, and I answer directly to the Illusive Man himself." Miranda said this coolly, as if she hadn't just essentially told someone she had raised them from the dead like a freaking miracle-worker. She sounded bored.
"I… you… what?!" Shepard managed to squeeze out the question, leaning back in her chair and letting her arms go limp. As the cogs in her brain started to mesh together, she leaned forward again, her elbows on her knees. "Cerberus? The terrorist, pro-human organization? The one that experimented on both their own people and unknowing test subjects, sometimes leaving them to die from those experiments? Are we talking about the same Cerberus?"
"Yes," Jacob replied, defensively. "We've unfortunately had a bad rap in the last few years. But Cerberus is the only organization ready to help you fight the Reapers."
"...the Reapers." Shepard felt a chill run through her spine as she whispered it. "Two years have gone by, and Cerberus is the only group that believes me? I hope to god you're wrong."
Miranda spoke up, crossing her arms and sounding annoyed, "You can discuss this with the Illusive Man yourself if you wish. He wants to speak with you when we land, which should be in a few minutes."
Shepard and Jacob shared an awkward glance, and the rest of the shuttle flight was silent, aside from the rattling of questions inside Shepard's head, and the threatening, mechanical hum of the engines.
Shepard was less than thrilled that this "meeting" with the Illusive Man was only through a vid-comm. The lack of face-to-face didn't help Shepard's automatic, though deserved, mistrust of Cerberus in general.
"Illusive Man, I presume?"
"Shepard. Good to see you made it out. I knew Miranda would get it done. We can't afford to lose you now."
"Look, I don't know what your angle is, but even if you did bring me back, I don't trust you."
"Your personal feelings aren't important right now. Humanity is on the brink of extinction, from a familiar foe."
Shepard grimaced knowingly, "Extinction? You mean the Reapers, don't you."
"Yes, the Reapers. We're at war, and nobody wants to admit it. But whole human colonies are disappearing, and we have reason to suspect the Reapers are behind it."
"Wait, you mean you haven't actually seen Reapers doing this?" Shepard's arms crossed in front of her as one suspecting eyebrow raised higher than the other.
"You've seen it yourself. Sovereign controlled Saren and the Geth. We think the Reapers are controlling whoever is abducting the human colonies. You took care of Sovereign, which is why we chose you. You are humanity's best chance for survival."
"But why go through the trouble of bringing me back? Why not talk to the council? Get help from the Alliance?" Shepard exhaled sharply, trying to stem the flow of questions trying to erupt through her mouth.
The Illusive Man exhaled a puff of smoke and tapped his cigarette. "Nobody is paying attention, because the attacks are random and happen in remote parts of the galaxy. Thousands of human colonists are disappearing, and while everyone else is turning a blind eye, Cerberus is doing something about it. We have reason to believe that they're targeting humanity because you killed one of them. You've got them scared."
Though he was starting to make sense, Shepard felt like he was still holding back information. His calm collectedness in the face of what he dubbed "human extinction" gave her an uncharacteristic urge to punch him in his cybernetic eyes. But she knew he had a point. She was probably Reaper Public Enemy Number One. She sighed and nodded. "All right. If what you say is true, that the Reapers are behind the disappearing colonies, I'll help. But I need proof." And this doesn't stop with Humanity, she thought to herself.
"Good," Illusive Man said lightly. He took a sip of his drink, his face inscrutable. "We think you will be able to find what you're looking for at Freedom's Progress, the latest colony to be hit. Find out what happened, if there's a connection to the Reapers. Jacob and Miranda will take you in a shuttle and brief you. If you don't find what you're looking for, we can part ways. But I think you'll find that we have the same goals in this, Shepard. But don't take my word for it. Go ahead and find out for yourself."
Illusive Man's image fizzled out, and Shepard's face morphed into a grimmace. She still didn't feel like any of her bigger questions had been answered. She was still waiting for a practical joker to pop out behind a corner and say, "Gotcha!"
She stormed up the stairs and went to the armor station to prepare for the trip to Freedom's Progress. Miranda walked up. "We're ready to leave when you are, Commander." Shepard slammed a fist on the holo display and stopped, staring at the wall.
"I doubt I still have any rank, Miranda." Shepard drew in a deep breath and slowly let it out.
"Luckily for you," Miranda replied, "the Illusive Man has put us under your command. Just say the word, and we can go."
That bit of information caught her off guard. She straightened up and turned around, rearranging her thoughts. She took another deep breath. "We can go to Freedom's Progress, but I'm going to need some answers soon, or I think I might just go on a murderous rampage."
"I would expect you have a lot of questions," Jacob conceded. "Hopefully Freedom's Progress will clear some of them up."
"Hopefully." Shepard forcefully emptied out her lungs and shook her arms out, trying to loosen up. "Alright." She looked at the two Cerberus operatives, straight in the eyes. "If I'm in command, I need to know that I can trust you both to obey any order, is that clear?"
They both nodded, and Miranda replied, "You have my word. We both took an oath to keep you alive at all costs. So far, I'd say we've done well."
Shepard raised a curious brow at Miranda's tone, which was somewhat mocking. "If you have a problem with me, Miranda, I need to know before we land."
"It's nothing, Commander. We'll get the job done. What are your orders?"
With narrowed eyes, Shepard promptly filed Miranda under her "suspicious" file. "We'll go down and search for survivors first. Then we see if we can find out what happened and who took the colonists."
Both Jacob and Miranda saluted, then headed back to the shuttle.
Shepard exhaled sharply, then whispered to herself. "This is just the day that keeps on giving."