The Illusive Man
The Illusive Man blinked once, twice, thrice and still didn't believe his eyes. Shepard was staying in his room, on his station, front of him instead of being on earth, getting his ass handed by the Alliance brass for killing thirty thousand batarians.
Shepard wasn't alone. His crew was accompanying him, or at least a part of it. No one was training a weapon on him, yet, instead they were looking at the windows. Taking the room and everything in it in. He wasn't really surprised by this. Everyone whom he had deemed important enough to see this room was like that in the beginning. One reason he choose to let this room build this way. Another one that no one could hide once he entered this room. Except if you were hiding above the room, and no one could get there.
No one he didn't want there at least. There was a way up there, a very secretive and long one with a door that only opens up to specific persons. And only he himself could do it. The door was programmed in such a way that only he himself could tell the door who it should let through. So far there aren't many people who could go there.
"Don't even think about it." Miranda Lawson spoke up as she noticed him typing something on the interface behind him.
"It doesn't matter anyway, Miranda." Shepard said. "His prized assassin and his best soldiers are dead or are getting killed right this moment."
One of the Illusive Man's eyebrows shot up at that as if to say 'what kind of bullshit are you saying'.
"It's not like he has an army or a few fleets himself." Jacob Taylor said in the following silence.
The Illusive Man now turned to look at Taylor as if to say 'are you sure?'.
The station choose that exact moment to shudder a bit from an impact.
"Joker! What's going on?" Shepard asked immediately.
"Cerberus suddenly appeared, Commander!" was the pilot's immediate response.
"EDI?"
"A contingent of Cerberus ships, mostly cruisers and frigates, entered a few minutes ago this solar system." The AI of the Normandy answered. "The explosion you certainly felt on that station had it's origin in the destruction of an Alliance fregate that was patrolling around near it when the Cerberus ships made itself know."
"What about the other Alliance ships in this solar system?"
"They are retreating for the time being. We also had no choice but to leave our designated place." EDI informed him.
"Damn it." Shepard swore.
"Looks like your plan didn't work out, Commander." The Illusive Man said smugly. "I think I have given you enough hints over the time we had worked together to not underestimate Cerberus."
"And despite all those hints and your overworldly might we are here now. Right here, in your own little sanctuary." Lawson pointed out.
"And now we can end the threat of Cerberus, even if we die." Shepard said.
The Illusive Man shook his in frustration. "Cerberus isn't me, Shepard. How often do I have to tell you that? Cerberus is an idea, a thought. Nothing that you can just easily destroy. Even if you kill me, it won't be the end of it. Someone else will pick it up. My death will change nothing."
"Not if we are eradicating you and your ideas from history." Taylor replied, waiting for a reason or the order to end his life, for now and ever. "With EDI on our side, it's possible."
"Not even EDI would be able to do it." The Illusive Man replied.
"EDI alone not, but with the help of Legion and the other geth's it would be possible." Lawson remarked.
"The geth have no interest in the life of the organics." The Illusive Man simply said.
"EDI?" Shepard suddenly called, surprising everyone.
"We are ready, Commander." The AI replied. "We are awaiting your orders."
"Please proceed with the plan then." he ordered.
"Plan?" The Illusive Man replied sceptical. "The Alliance wouldn't be moving on the whims of one lousy ex-marine of theirs."
"Who said I was talking about the Alliance?"
"Who else could you be talking about, Shepard?"
Before anyone could say something ships started to explode. Cerberus ships to be exact. The Illusive Man couldn't stop himself from turning around and looking out of his window, looking for the reason and once he found it, he didn't believe his eyes. The flottile was there. All of the quarian ships, armed with weapons, even the civilian ships as far as he could see and they were taking out his armada.
"Your biggest mistake was to give me so much power." Shepard remarked at his back. "I mean, Miranda, Jacob, a new Normandy and an AI with connections to Cerberus to boot. Either you are way to sure of yourself or you really never saw this coming. This is the end for you and Cerberus."
And for once The Illusive Man believed him. That he had really given him too much power. That for once he had made a mistake. That he had been for once to sure of himself. That he had believed himself to be able to tame this wild cat. But as it came out the beast had tamed his men and used them against him. He really hadn't seem that coming.
Shepard didn't wait any longer. He trained his pistol on the Cerberus head and pulled the trigger three times. Head, heart and lung.
With his last breaths The Illusive Man cursed the Commander and his own mind for not preparing himself for this outcome.
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A/N: I'm sure The Illusive Man did plan against that kind of behaviour of our hero/heroine, but with EDI, Jacob, Miranda and the Normandy's stealth system and Joker as a pilot Shepard could have pulled this off. The quarians are not friends of Cerberus. If given the chance to anihilate them, once and for all, I'm sure they would take the chance and that's what happened here.