Board Thread:Questions and Answers/@comment-212.35.14.225-20150704132426/@comment-6512-20150909163027

Those points are all easily explainable though. You seem to have missed where they state it was thanks to the Medic's "heightened state of consciousness" during his coma that they were able to implant all those things into him. That suggests it wouldn't be an easy thing to do to any other person. Big Boss even says he was "the best man they had," and a chunk of his combat training would have come from the man himself prior to the blast, while he was with MSF. It's not like the guy was some nobody.

By the time of S3, the AI Patriots were fully in control. They might not have known about the whole Phantom Big Boss ruse (my memory is fuzzy), so S3 could even have been their attempts to replicate the idea, or just something they came up with on their own. But the AI's do also admit that the Solid Snake Simulation that Ocelot described wasn't really what S3 was, so I don't think there's any point acting as though he was being truthful.

I'm going to have to go back and re-experience MGS4's recap sequences again to fully get a grasp on the whole thing, but I don't think they're lying to him. I think it's a bit of a stretch to say that. They're just telling him what he needs to know. Zero created the Patriots AI, which are fuelling the War Economy. Their purpose is to destroy it. Snake's intention throughout MGS4 is never to stop the Patriots, he only wants to stop Liquid from using GW to infiltrate the Patriots. It's only when he gets to GW that Naomi reveals she had a plan to eliminate the Patriots. Snake was always being used in MGS4 ("Snake, one of the names is our biggest contributor!") That's what makes Big Boss' speech at the end to him so poignant. With the Patriots gone, Snake can now live life how he wants. He was always being used. This isn't some new revelation.