I like how half of MGS4 makes even less sense now.
"And so The Patriots... I mean Cipher, we were Cipher until we started the AIs, which were actually The Patriots... we all had differing views of how to fulfill The Boss's will... except Big Boss, who actually stopped liking The Boss's will after this thing happened involving something called Peace Walker. Anyway, that was the start of the war between Zero and Big Boss... except they really only fought when Pacifica Ocean stole Metal Gear ZEKE, because like that right after that, Big Boss was put into a coma by a rogue underling of Zero's, and Zero decided to protect Big Boss with this crazy scheme - more on that later - and then he went into a vegetative state because of parasites before Big Boss woke up again, I think."
*later, at the graveyard*
"...and so that's how both of Otacon's parents are actually responsible for not only all Metal Gears, but also The Patriots AI. Weird ass coincidence, huh? Anyway, this is the third time you've erased me... well, second, technically, because the first time it was a fake me with plastic surgery and brainwashing. Wait, don't get mad, Snake, I know it was the defining moment of your life that scarred you forever, but it was really important. Besides, he had a robot arm, brown hair, and a horn. I don't know why you didn't notice, since I trained you in FOX-HOUND and I didn't look like that. Did you assume that I suddenly got in a really bad accident but only because self-conscious about greying hair? Hell no, the ladies love this silver fox. Anyway, yeah, I guess someone should have mentioned that there was a second me running around."
"You see, Snake, it just goes to show that anyone can be molded into anyone. I know you told that Raiden kid that that's a horrible idea that can't really be done, but you can. As long as you have magical plastic surgery and brainwashing technology. I guess that last part kind of undermines the moral, but... What was that guy's name...? He might have originally been black or something; it was crazy how much they made him look like me, but couldn't just sand down that horn. Anyway, you'd think that if Cipher in the 1980s knew all about brainwashing and Ocelot's self-hypnosis techniques, then the genius supercomputers of the 2010s that run the world would realize that Ocelot of now was probably pretending to be Liquid, but I guess they forgot or something."
"Speaking of Liquid, I dunno why he apparently said that I 'chose' him and called him inferior. I asked about this from Venom - this was my body double, by the way - and he apparently treated him super nicely for a couple months. Weird. Anyway, he also became friends with little Psycho Mantis, who as a child could actually pilot Metal Gears with his mind, namely a Metal Gear created by Otacon's dad that little Otacon was supposed to be a test pilot for. Again, wacky coincidence, I know."
"Oh, and Kaz was my best friend... Oh, Kaz? You know, Miller? McDonnell? No, his name was Benedict Kazuhira Miller. Half-Japanese? Missing an arm and a leg? Constantly paranoid and pissed off at everything? You don't remember any of this? Guess he mellowed out or something. Though I can't blame him for being pissed, I had this big speech with him about how we'd face the whole world together no matter what, and then I took a nine year nap and the second I woke up I left him high and dry with no explanation. I mean, I might want to take on the whole world, but try getting nearly blown up! I wasn't going to face all of our enemies, like... Skull Man, or whatever. I don't remember if there was anyone else after us. I told the fake me that it was the whole world after him, but I think it was just Cowboy Voldemort. Hmmm. Might have oversold it. Anyway, he managed to take down Skullomania and build up a mercenary fortress while still being in the world's eye so... not sure why it was so important for me to be in hiding to do that. Actually, now that I think about it, I don't know why we didn't give him plastic surgery again to be someone different afterwards. I kept waiting for someone to ask how I could be in America running FOX-HOUND while a guy who recruited people solely on the basis of saying 'I'm Big Boss' was running around the world, but nobody thought twice of that, I guess."
"Anyway, zeroes and ones, no snakes, yadda yadda." [hands Snake cigar]
"This is good, isn't it."
... *sigh*
Yeah, Metal Gear Solid's continuity is a dud.