Decoy "Octopus"? "Wouldn't something like 'Chameleon' be a better fit?" some might ask. It's relatively common knowledge that chameleons are actually poor at camouflage; their color-changing process takes minutes on end, and they tend to change more based on mood than environment. What might be less commonly known is that a particular species of cephalopod aptly named the "Mimic Octopus" is arguably better than any known animal on Earth at the art of disguise. Not only can it change its color in seconds, but it can change its shape, skin texture, and position of its limbs to impersonate numerous sea-dwelling creatures. It's also highly intelligent, not just mimicking the appearance of other animals, but doing so based on the situation (for example, if attacked by a damselfish, it will mimic the banded sea snake, a predator who feeds on damselfishes). Sounds a lot more like what Decoy Octopus is capable of, more so than a chameleon. And the animal was discovered in 1998... the same year that Metal Gear Solid was released.
Why does Snake not want to see a woman die in front of him? Answer: He saw Gustava Heffner from Metal Gear 2: Solid Snake die in front of him by Metal Gear D, the canonical fourth Metal Gear. It's why he goes out of his why to see not Meryl die.
Frank Jaeger, Gray Fox, being Naomi's adoptive brother may seem to come out of nowhere, but there are hints. Firstly there's her extensive knowledge of how he was cyberized, and look at her last name, "Hunter." "Jaeger" is German for "Hunter."
This technically only applies to The Twin Snakes, although this was also mentioned in the Japanese script for Metal Gear Solid, as well. Anyways, Psycho Mantis's line of "It feels so... nostalgic" in regards to performing a good deed for Solid Snake and Meryl Silverburgh before dying seemed very confusing to some fans... until you remember that Psycho Mantis's mother died while giving birth to him, which meant he was referring to what his mother did for him before dying. Stated as such by Kojima here: http://muni_shinobu.webs.com/mgs/commentary2.html
Also, it seems odd that it required a bribe to persuade Donald Anderson to build Metal Gear REX, especially when he believed in nuclear deterrence and would have allowed for it to be built anyways even without the bribe. However, when you remember that he was Sigint, and that he had a nightmare referring to Metal Gear, it suddenly makes a whole lot more sense as to why he'd have to be bribed.
It's more likely that, as a core member of the Patriots, the bribe and persuasion needed were for show. Remember that while Armstech is developing REX and desperately needs the money from the government, and Solidus considered REX his tool against the Patriots, the Patriots were always aware of the project.
At one point, Revolver Ocelot mentions being impressed by Snake's skills, and says something to the effect of "Just what I'd expect from someone with the same code name as the boss." The first time you play the game, it's obvious that "the boss" refers to Liquid Snake, who Ocelot was working for at the time. Then comes Metal Gear Solid 3: Snake Eater, where we learn that Big Boss (who Solid Snake is cloned from) once went by the codename "Naked Snake"... and that Ocelot knew him during this time. Maybe it was intentional, maybe not.
It probably refers to Liquid Snake. Whenever Mantis or Raven refer to Liquid, they usually call him "boss". At best it would be a double meaning, because both Liquid and Solid have the same code name as Big Boss, and both were cloned from him.
Not to mention the sheer, and utter mixture of Hilarity and Horror that the entire Shadow Moses Incident can be caused by someone having a major jealousy-inducedtemper tantrum taken up to eleven, hilarious because the motive was because Liquid didn't like being the "inferior" brother, and horrifying because of just how easily someone that unstable can take over a nuclear disposal site and hijack a Metal Gear - Shini
Ocelot's hidden conversation at the end implies this was all part of the plan. Sprangitudinous
This not-troper always liked the MGS games, even with the long and wordy cutscenes, but always felt that some elements were a bit... off. Then he realized that MGS is a Deconstruction, not just of movie and video game tropes, but of the entire medium of video games. Everything from the fourth wall-breaking Codec calls to the perfectly straight tutorials to Psycho Mantis' mind reading and psychokinesis to GW urging Raiden to turn off the console is part of an attempt to show what games can get away with in the name of fun, without banging the players head with it or turning into a total parody. And the way the endings for each entry in the series got steadily more depressing was an incredible setup to the amazingly heroic finale of MGS 4. —Not a troper, but I use the screenname "Bad Username" frequently.
In Metal Gear Solid, Snake talked about how virtual training is no substitute for real life experiences. At first, I thought it was just him talking about how he had actual battlefield experience, making him more skilled. Then I realized: what is the definition of a Video Game? This line is basically Hideo Kojima saying that just because you can do surgery or practice law in video games doesn't mean you can do it in real life. The game is basically telling us to not play it too much.
After playing MGS 1-3, and reading the comics for 1 & 2, I read this page, lo and behold the light shines brightly. What the troper above mentions about Liquid's tantrum, makes it weirdly plausible that Solidus anticipated that the two most dangerous individuals to his plans were unlikely to be easily eliminated-unless the killer was one of the brothers. Given that Liquid and Solid are on a whole new level compared to any other soldier alive at the time, it makes sense for Solidus to set them up to kill each other. The only way he could pull this was to isolate them from society, place them in a perceived high stakes situation, wait for a body, and nuke an already irradiated island, safely in the knowledge that he could blame the detonation on terrorists mishandling the warheads. It further makes more sense when we examine the presence of a Metal Gear, its the only prize big enough to get Liquid there, and scarier enough for Solid to come out of retirement. The sheer size of Rex makes covert transport from such an isolated area, quite difficult, and despite the complexity only the plans are necessary for Solidus to build a Rex in new location. Nuking the island destroys any records of Rex. Kills the CEO and DARPA representatives who knew about Rex. Removes the Next Generation Special Forces who were slowly coming apart genetically(covering up that little not so legal experiment), wipes out Fox Hound which seems to be a pointless liability given its tendency to do The Starscream to the US GovernmentUnited Nations unlucky bastards stuck with telling them what to do. Foxdie is the chancy bit however, as Solidus's ace in the hole required someone he did not have complete control over to seek vengeance at a jeopardise-the-entire-mission level. Ocelot's selling of the plans is just his Chronic Backstabbing Disorder, something Solidus could not stop (and probably anticipated) as he needed Ocelot to rig this Gambit Roulette, hence why Ocelot does not show signs of Foxdie (Haven't played MGS 4 but if he does turn out have Foxdie then it kind of changes Ocelot into Snake Plisskin from the second movie...). I nearly wrote off my computer with a glass of coke when this clicked ;)- Eyclonus** And the phrase "code". It refers to both codename, and genetic code. - pinkdalek
The Phantom Pain adds a further layer as to why Liquid would continue to trust someone seemingly as unstable as Mantis can be when Mantis proposes the idea of having Decoy Octopus pose as the DARPA chief following his (actually planned) death at Ocelot's hands. They've probably worked together for years since 1984, and Liquid actively owes Mantis his life. Mantis, meanwhile, is psychically shackled to Liquid given his bubbling hatred for Snake and Big Boss, as per the new information regarding how his abilities work.
A bit of fridge creepiness. Before the the Psycho Mantis fight in MGS, there are a couple of unsettling details. 1. The door at the end is closed. 2. Once Meryl becomes possessed, you notice that the first person view is.. third person - through a mask of sorts. That leads me to conclude that Psycho mantis is in that hallway, stalking you. It also points it out as when you enter the commander's room, the door waits for a second (perhaps someone's in the doorway?) until he comes inside. Creepy.
Yes, another problem with the whole Gene issue. Not one about the whole Dominant/recessive argument, but rather a problem with the Genetic issue and FoxDie. FoxDie was programmed to target people with specific gene patterns. So why in the hell did Liquid think that because he would be safe if Snake didn't die? The whole problem between the Dominant/Recessive thing is that Liquid and Snake can't have the exact same genetic pattern, not unless they wanted a whole string of carbon copies in the first place, which was not what they were looking for. Sure, Naomi could, and would program the virus to kill Snake, but if a non-hostile party had programmed/injected the virus into Snake, there's no guarantee that Fox Die would kill both of them.
Liquid thought he'd be safe because Liquid really doesn't understand genetics. According to Kojima, Liquid just plain doesn't know what he's talking about.