That's a shitty analogy. How about this one? You'd be stupid to trust Cerberus.
BUT LORD RAINE THE ILLUSIVE MAN DIDN'T KNOW
Yeah. He claimed. But then again, Jacob clearly outlined a situation in the Alliance in the very beginning of the game where Alliance born and Alliance bred humans did off-the-books work for the Alliance so the Alliance could get things done (like assassinations) without 'actually' having to do them. Their dirty laundry gets cleaned, and if shit ever goes south, they disavow all knowledge and say you're a rouge element.
What did the Illusive Man do when you pointed out all the evil shit Cerberus has done? Well, he said things had changed. And when you pressed the issue? He said he knew nothing about it and claimed they were rouge elements.
That's a hell of a familiar excuse, isn't it? Didn't we just hear that story about the Corsairs about five minutes before that? We did.
Fact: The Illusive Man handles the money and the direction of the organization. He's the one who sets up the projects, and he's the one who writes the checks. Practically speaking, it's pretty much impossible for a section of Cerberus to literally 'go rouge.' They would lose all access to their resources, and the rest of the organization would swoop in under Illusive Man's orders to crush them, because he knows who they are, where they live, what they look like, and exactly how to track them down. So unless they're all giganinjas and managed to set up a billion intergalactic lemonade stands while nobody was looking, the scenario claimed is pretty much impossible.
That only leaves one real explanation left. He knew, he funded it, and when shit went sour, he cut them loose. Hell, the entire Cerberus organization is founded on that. Look at how they're organized. Cells that know nothing about each other, have nothing to do with each other, and work independently from everyone else. The only one who knows everything that's going on is the Illusive Man. No one else exists who could corroborate any story or evidence. The left hand doesn't know what the right hand is doing, so if the left hand gets cut off one day, the head can feed the right hand whatever story it wants.
BUT LORD RAINE THE RECORDINGS ON JACK'S MISSION SAID THE ILLUSIVE MAN DIDN'T KNOW ABOUT IT
And the Illusive Man said when the mission was over that he was "disappointed that the Cerberus cleanup teams had apparently missed data logs."
Do note the important thing here. Cerberus, specifically Cerberus operatives under the control of the Illusive Man, got there before you, before anyone, and cleaned the place out from top to bottom. That means any and all evidence in that facility is potentially planted. Isn't it rather odd how the only logs left are the the exact ones that manage to completely vindicate and clear the Illusive Man? And isn't it odd that the ones they allegedly missed were on computer terminals sitting out in the open in major intersections of the building? What are the odds of that?
Way too long. Way, way too long.
BUT LORD RAINE AREN'T YOU JUST BIASED AGAINST CERBERUS?
Aren't you? They were planting Dragon's Teeth onto out-of-the-way colony worlds to observe the effects. They were sending out Rachnai into areas garrisoned with Alliance military personnel just to observe how the Rachnai fight. They planted fake distress beacons in the middle of Thresher nests just to gather data on them, at the expense of two entire companies of soldiers. They assassinated Admiral Kohaku and threw his body into a pen filled with husks just for the hell of it. They injected the acid venom of a Maw into a marine's blood "to see what would happen."
Are you seriously going to try and tell me that all of that was 'just rouge agents?' Either the Illusive Man is the most incompetent manager EVER, or he's lying out of both sides of his mouth at the same time, and trying to bullshit you for every last bit he can take you for.
The Illusive Man has intel detailed enough to know the exact measurements of every member of his organization. Are you seriously going to pretend that entire cells could go rouge and do these massive operations, and for him to not know anything about it?
To be blunt, I'm not even sure Wilson was a traitor. I think the entire thing was a setup by the Illusive Man, who was getting impatient that your reconstruction was taking so long while more and more human colonies were disappearing. I don't believe that the Illusive Man didn't know. He flat-out stated that Wilson was one of his most trusted operatives. I think that either Wilson was under orders to do it, with the intent of speeding up the process and giving you a trial-by-fire, or that he was always of that caliber, and the Illusive Man, knowing it, manipulated him into doing it, again for the purpose of speeding up the process and giving you a trial-by-fire. If it's the first one, arrangements were probably made to get Wilson off the station and hide him until everything was over with. The miscalculation was Miranda showing up when she did. The Illusive Man didn't want it to happen, but as he himself stated, "Miranda acted as I expected her to."
BUT LORD RAINE-
Hypothetical Opponent, Imma let you finish, but Word of God is with me on this one too. The Illusive Man, and I quote, "represents both the best and the absolute worst of humanity in one package." That means he's self-sacrificing, a patriot, and a man of his word. It also means he's a lying liar who lies lies, is willing to sacrifice as many lives as it takes to get what he wants, has no compunctions or moral boundaries he isn't willing to cross with impunity, and will cheerfully and without hesitation betray and screw-over anyone and anything that starts messing with him and his bottom line, up to and including entire species, the Citadel, the Council, the Alliance, his own organization, every last person under his command, and you, Commander Shepard.
"Why is the Illusive Man after Shepard in Mass Effect 3?"
Bitch, I'm surprised it took him this long.