These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Mantis' persistant refusal to believe in the existence of ghosts (despite great evidence to the contrary) became even funnier after the release of Metal Gear Solid 4 where Mantis appears...as a ghost.
Magnificent Bastard: Despite early appearances to the contrary, Ocelot is still one of these here.
Mantis: But it's all about the little details! I mean, you must spend every day pretending to act like you're falsely letting on that you aren't not unbetraying someone you don't not purport to allegedly work for but really do! How do you keep all this shit straight without having an aneurysm?
Ocelot: * shrugs* Practice.
Saladin (Big Boss) is almost certainly one of these too, with his extreme fondness for plans, especially when it comes to manipulating Liquid. Not to mention his general badassery.
Tear Jerker: The fate of Berthold. The penultimate comic, which shows us the dead bodies of all the main characters (excluding Ocelot), might also count.
