Author's note: This is where things start to really change. Also, you guys will probably begin putting things together from here on regarding Shepard's backstory. I didn't start out with this as my original idea on how the story would go, but it just seemed to fit together. Let me know what you think when you figure things out. Shepard's confrontation with the Illusive Man comes next chapter.
Jacob was anxious. When he started working with project Lazarus he thought bringing Shepard back to life was an amazing idea. He still thought that, but now he wasn't so sure the rest of the plan would work out. Was it really a good idea to bring Shepard into direct contact with the center of Cerberus operations?
Why would Shepard want to work with Cerberus?
Jacob was not a fool. He heard the rumors and investigated the reports. Every Cerberus outpost Shepard wandered across was destroyed. Every Cerberus operation busted, every Cerberus agent slain.
He stilled. He ran that thought back through his head.
Shepard destroyed every Cerberus installation she had come across. She killed every Cerberus agent, even going out of her way to hunt down the last survivors. He looked down. He was wearing a Cerberus uniform. They were about to dock with a Cerberus station.
What made him think that this encounter would be any different?
They had almost a hundred crew and agents aboard. Security systems. Defense mechs. But Shepard had a gun. She could probably take down everybody on Cronus station even without one. She was also carrying Wilson's severed head. Was that supposed to be a message to the Illusive Man? Was that what an Omphalos stone was? He vaguely remembered something about giving someone a horse's head as a threat. Was this similar?
Wait, she cut Wilson's head off with her knife, so where did that hacking blade she was using earlier disappear to? Did she leave it behind? Was she hiding it? He didn't remember. He eyed Shepard carefully. She could be hiding something behind her back; she was known to pull knives out from all kinds of places. Marines love to talk about things like that, and Jacob always felt that this was the exact kind of important detail Miranda would never recognize as vital information.
Were they all going to die? Were they bringing their own death with them?
Jacob resolved to keep an open mind; perhaps this time Shepard wouldn't kill all the Cerberus agents on the station, then blow it up. Regardless, it never hurt to be prepared. All he needed to do was stay on the opposite side of the station as Shepard, keep an ear out for gunfire and the agonizing cries of defeat coming closer, and prep a shuttle for him and Miranda to escape away on. Just in case.
Jacob left them at the hangar, citing maintenance work that needed doing. He saluted Shepard and then departed. Quickly.
Shepard left Wilson's head in the shuttle.
Miranda and Shepard walked through Cronus station. They passed through the corridors in silence, then they went through a series of blast doors into the heart of the installation. In front of them was an anachronism; a pair of wooden doors on hinges. Brass fittings and handles gleamed softly in the light. Miranda gestured ahead of them, "Shepard, the Illusive Man is behind those doors."
Shepard made a small sound in the back of her throat. Before the doors was a small table. On the table was a dark wooden box. She knows this box. She remembers who it belonged to. Shepard slowly reached out with a shaking hand, and opened the lid.
Inside the velvet interior lie two knives.
Steel. Folded. Clay-tempered. Cold iron, pure silver, and raw gold fused into the blade, guard and pommel. Shepard knows these knives. They belong to her.
Shepard takes the knives, and hides them behind her back. She rests her hands on the doors for a moment. She knows these doors, too. They are cracked and worn from time and battle, but at her touch, they welcome her back. She takes a deep breath, opens the doors and strides inside the true heart of Cerberus.
The room is large, barren. There is just a chair facing the window that takes up the whole far wall. Out the window lies a star, roiling with energy. A man stands next to the chair. He turns, faces Shepard.
Shepard walks slowly at first, then faster and faster, until she is running at him. She throws her arms around him, and buries her face in his chest. Hugging the Illusive Man, the leader of the organization Shepard has opposed and ruthlessly hunted, Shepard starts to cry. In the doorway, Miranda has no words.
The Illusive Man glances at Miranda, and motions for her to go, leaving him and Shepard alone.
They hug for several minutes before Shepard is able to control her tears.
Miranda stands outside the doors to the Illusive Man's sanctum. Her brain still cannot process the image of Shepard hugging her boss. Time passes, until the muffled sounds of conversation and laughter through the doors snap her out of her daze and she turns and walks towards her office. Maybe things would make more sense after coffee.
After coffee, things still do not make any sense.
Sitting at her desk, Miranda pulled up her research on Shepard's history and cross referenced it against all the data she had on her boss. They never met; they were never even in the same system as each other. At no time did their paths cross. Shepard never received any correspondence from the Illusive Man; there wasn't even a trace or hint of any kind of communication between Shepard and anyone connected to Cerberus. So how did they know each other, let alone to the point of friendship?
Miranda frowned. Shepard had hugged the Illusive Man. Tears were involved. That showed a level of familiarity beyond friendship. A mentor? Father figure?
She reviewed the information she had on Shepard's parents; nothing. She always hit walls when trying to dig into Shepard's earliest years. It was as if Shepard just appeared out of thin air. She always figured the Alliance covered up Shepard's family somehow, but now... could it have been her boss that did the cover up? Their DNA had no matches, so he wasn't related to Shepard.
But still, that hug. The way she seemed so happy to see him. As if she never thought she would see him again...
Miranda reviewed her boss's history again. Maybe if she approached this from his side, things would become clear. But back then he showed no interest in Shepard at all. It wasn't until she survived the ambush on Akuze that Cerberus made any note in Shepard, and all of the Illusive Man's inquiries into Shepard were standard queries. Things didn't change until Shepard became a SPECTRE, and everything she did since then Miranda already went over with a microscope. Twice.
Then how did they know each other? When did they have the time to establish their obvious strong bond?
She drew a quick timeline of Shepard's life. There was nothing showing any recognition from either of them regarding the other before Shepard survived the ambush on Akuze and became an N7, so she could ignore what happened before then. Sometime after that point her boss found the time to become good friends with Shepard, but before Shepard became a Spectre.
She blinked. Shepard didn't know Jack Harper was the leader of Cerberus until she just now when they walked into his office.
So. At some point her boss had found the time as Jack Harper, not the Illusive Man, to become at least friends with an N7 marine without ever coming into contact with her. Miranda's records of Shepard were the most complete for this periods. All her deployments. Her vacations to various alien planets, her trips to museums and historical landmarks. Even the ridiculous lists of books Shepard somehow found time to read. Nothing showed any time for any interaction with her boss.
Yet another complete mystery surrounding Shepard to add to the already existing pile. Miranda was the foremost expert on Shepard; during her time as director for the Lazarus project, she collected every scrap of data pertaining to Shepard's life. Her near photographic memory helped her put it all together, shaping an image of Shepard's true nature. Except that wasn't true; she never had a solid feel for Shepard, and since Shepard came back to life Miranda felt she had less and less of a grasp on Shepard's true nature. Shepard just didn't do things like any other person. Ever. For example, Shepard's consistent trips to museums even though it was plainly obvious she didn't like museums. Her interests in ancient myths and legends, which she never actually did anything with. No other N7 had even remotely similar interests compared to Shepard. It didn't fit the personality type. It actually didn't fit models of Shepard's psychological development either.
And what was all that about that box? Shepard recognized those knives, but they were relics from earth, at least 400 years old. Miranda didn't know much about them but they were some of the Illusive Man's most treasured possessions. Yet Shepard held them as if she intimately knew them, despite the fact that they were in the Illusive Man's possession for longer than Shepard was alive.
Maybe she needed something stronger than coffee.
She saw a message from Jacob appear on her omnitool.
'Did Shepard kill anyone yet? Do you need an evac?'
This was no time for frivolity. Frowning, she fired off a quick response.
'No. She gave our boss a hug. Like they were long lost relatives.'
Jacob's response came back immediately.
'Even worse than I feared.'
She definitely needed something stronger.
The door to her office opened. Shepard stumbled into Miranda's office.
Miranda quirked an eye as Shepard slouched into a chair. Shepard didn't look at Miranda, but stared at the ceiling.
Several minutes passed.
Miranda went back to work while keeping an eye on Shepard.
Several more minutes later, Shepard shook herself, and sat up.
"Jack wants you to be my XO."
Miranda turned to Shepard, and raised an eyebrow at her.
"Jack Harper, the Illusive Man."
Of course Shepard would know the Illusive Man's real name. Proof that they knew each other from somewhere.
Miranda nods.
"He also wants me to take over your training. Teach you everything I know."
Miranda was nodding before Shepard's words caught up with her.
What.
She froze for a moment, then licked her lips. "Does this mean you're going to be working with Cerberus?"
Shepard nods.
Miranda stared at Shepard. Shepard stared back.
Miranda clarified, "You are totally fine working with us."
Shepard nodded. "Yes."
Miranda snorted in disbelief. "All the experiments you stopped. What happened on Akuze."
Shepard waved her hand dismissively. "Meh. Not that big a deal."
Miranda kept staring at Shepard.
Shepard shrugged. "What? I wasn't mad at Cerberus for what you guys did. I've been friends with worse people. No, it was how you went about doing it that I didn't like."
"The experimenting on people? The bombings?"
"It was mostly the fact that you called yourselves Cerberus, honestly. I always felt it was disrespectful."
"Disrespectful? To what, a Greek mythological dog?"
Shepard waved her hand dismissively. "Nah, I once knew a place called Cerberus. I have a lot of respect for it, and didn't like you guys calling yourselves Cerberus." Shepard grins. "The doors to the old man's office are from Cerberus - the place, I mean."
The old man? Miranda nodded. More confirmation they knew each other well. "So now you have no problems with us?" Miranda clarified.
"Not really. Some of the stuff you guys did is a little questionable, and certainly reprehensible. Other than that, no."
"But we have recently shifted focus from being a humanity first organization to doing anti-Alliance operations. Doesn't that bother you?"
Shepard shook her head. "The Alliance are the bad guys here. Sometimes you have to do some bad things to bad people to stop those bad people from doing even worse things. I get that."
"What."
Miranda couldn't believe Shepard. One face to face conversation with the Illusive Man could do this?