Wasn't it suposed to be a 'surprise' that Big Boss was the leader of OH?

Well, on the surface it's not easy to see why. Instead of facts, I'll answer your question with what I hope can be considered reasonable assumptions.

The Patriots aren't people, they are an Artificial Intelligence system. So the 'artificial' part is firmly established, the intelligence - not so much. So that's one possible reason. But it should be noted that Big Boss wasn't a genius. He was just the best soldier they ever had. He was aware that he was being used by the end of Metal Gear Solid 3, he may not have been aware while being used other times after that. 'Liquid' Ocelot, a man who clearly wanted to burn the Patriots at both ends, managed to take over what amounts to the entire world military, and not only was he not challenged, he appears to have gotten everything he wanted with little resistance. So it's my 'reasonable assumption' that these two men weren't stopped because they gave the AI exactly what it was looking for. Perpetual war. In fact Big Boss was dead-set on it, apparently. So even if these men want to destroy the Patriots they are 'incapable', the patriots thought.

And I guess on some level it was true. If it weren't for what Sunny did at the end of MGS4 Snake killing Ocelot probably would have changed nothing at all. So I would assume the Patriots felt comfortable using them because they felt invincible.

It's still a pretty shaky scenario though, and I haven't gotten to the end of Peace Walker yet, so my opinions could change on why things are the way they are, but I think that's fairly logical.

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You can't know what you're talking about if you don't know what you're saying.

Nope! Just finished the story, and the truth is much simpler and definitely more clever. - Before I get into it, I want to bring up how shocked I am by the lack of concrete plot holes in a story as convoluted and massive as Metal Gear. The mythology has a chronology that's more aligned than the books of the Bible. -

Anyway.

It's not like he announced it to the world, there's no big speech or anything; on record, at the Pentagon, unless he has moles - and his men are supposed to be loyal. He doesn't run 'Outer Heaven' at the end of Metal Gear Solid: Peace Walker. He runs Militaires Sans Frontieres. A 'separate' organization. The name 'Outer Heaven' is an in-joke reserved for close confidants and later his army, but never 'outsiders'. He's basically a cult-leader, and his followers will embrace his every move. So he creates the 'Outer Heaven Uprising', and some of his Militaires Sans Frontieres comrades follow him into it... 21 years later. Provided the term was hardly ever used since that speech; even his own guys (save Miller) would have no real reason to remember it at all. Their kids are old enough to drink by the time it happens!

The question then though, is what kind of fall out, or falling in (with Zero), causes the Big Boss to run to Foxhound? Maybe he used the excuse that he wanted to be close to his children, maybe Zero made him disband his army to prove he was serious? Who knows. Whatever the case is there, he certainly used his position as leader of Foxhound against the government, and his 'son'. So I'd say the Patriots accepting him in was a bad idea. Then again that might be where this whole 'perpetual war' thing comes into play, so Zero or the Patriots might very well have been using him, knowing full well that he would betray them and try to begin an organization bent on endless conflict. (Which isn't a far cry from his original organization, but they were still basically just mercenaries.)

I'm sure if we ever get remakes of the first two Metal Gear games it will follow a plot something along those lines, provided those additional questions are answered.

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You can't know what you're talking about if you don't know what you're saying.