20. MGS3 Keeps Track of all Your Kills, Makes You Face The Dead In A River
This is a very cool part of MGS3; the game keeps a count of every killed enemy, and how you killed them. At a certain point in the game, Big Boss finds himself in a dream-like sequence in which he is wading through a narrow, ghostly river. As he is wading, he must avoid every single enemy he's killed until that point as they reach out to grab him. If he slit their throat to kill them, their neck is now spewing blood and so forth, while sometimes they may even moan, "You ate me!", but this is only achieved by killing an enemy, letting a vulture chew on the dead body, shooting the vulture, and then eating it. Crazy!
19. Liquid Snake's Mind In Revolver Ocelot's Body Via Arm Graft (MGS2)
This is by far the weirdest thing I can think of in the Metal Gear franchise. It goes like this: Revolver Ocelot had his arm chopped off by one of the ubiquitous cyborg ninjas, Grey Fox in the first MGS game. Luckily, Liquid Snake has an arm to spare, since Solid Snake killed him at the end of that game. Inexplicably, Liquid's will and consciousness remained in his newly grafted arm, which takes over Ocelot to form Liquid Ocelot once the arm graft is complete. So, Liquid's mind is dominating Ocelot's body, and while this is properly explained in the last minute of MGS4, it's still a ridiculous twist.
18. Old Snake Is Responsible For Drebin's Monkey's Smoking Habit (MGS4)
Solid Snake loves to smoke. When he becomes acquainted with gun-dealer Drebin and his monkey, the monkey decides to take up smoking to emulate Snake, because he's just too badass and all that.