MGS4 didn't even seem like it was in the same universe as MGS2, like it was not connected to it whatsoever.
Nanomachines, son!
Everything with the S3 plan was just ignored and was barely even acknowledged. It was never explained how humans even receive orders from the A.I.s at all which always bothered me.
I'm pretty sure the nanomachines were responsible for that
Sure it's probably them just manipulating digital information to enact their will, but it was never actually stated. MGS4 was very lazily written, and the whole Johnny & Meryl thing has got to be the most embarrassing moment I've ever seen in gaming.
Please refer to the above answer!
Johnny should of stayed a B level character that just made cameos.
But, the nanomachines made him more awesomer than Snake in the end
MGS is the most perfectest series ever. Most of the fans say so - I read it on the Internet - so I believe it must be true.