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What you see is what you're being shown
When I make a point of telling you that videogames aren't real, I honestly don't mean to insult your intelligence. You realize that the "worlds" presented within videogames are fictitious, and so do I. We tend to suspend our disbelief for the sake of the experience, and imagine them as a sort of alternate dimension to our own, following its own internal logic no matter how insane. In this sense games are no different than fictional movies, TV shows, or novels; we pretend its real so we can enjoy it.
You're also smart enough to know that, unlike other mediums of entertainment, videogames require participation from the player, which allows them to create a deeper sense of immersion and realism once we do decide to suspend our disbelief. Whether we're commanding vast armies from a lofty bird's-eye-view or witnessing everything through the eyes of a single person, every virtual "universe" we explore has the power to suggest a level of believability that linear, passive presentations of fiction cannot because the worlds in videogames are dynamic, interactive, and obey rulesets. Books do not allow you to test a hypothesis of what would happen if you did something differently, although they may describe things as being much more dynamic than what is possible in a game. Videogames allow you to personally meddle with notions cause and effect, and in the case of a series like Metal Gear or Grand Theft Auto, cutscenes handle the more complicated stuff, reinforcing the illusion that the world is real, even if you don't personally get to do a lot.
Of course, that's all that it is: an illusion. What you see is what you're being shown, created by a team of artists whose job is to create that illusion for your enjoyment. It's more fun to pretend that the simple textures and polygons which combine to resemble something similar to a tree in the starting area of Mario 64 outside the castle is actually a real, leafy plant that grow out of the ground; that the clouds in the sky are actual masses of water vapour and crystals suspended in the atmosphere; and most importantly, that Mario is indeed person who jumps and runs and goes "Yahoo!" when he does flips onto the heads of evil mushrooms. But none of these things are so. If somebody were to tell you that Mario was a real person who had feelings and could speak, you would explain to them that there are simply a limited set of pre-recorded sound files stored on the cartridge which are pre-programmed to play when certain events are triggered, such as pressing a button. "He" will never say anything that isn't stored on that cartridge.
And if you ever want to think critically about a work of fiction you'll need to keep the illusion in mind.
Once upon a time, and then something else
As the colorful characters in my trusty high school day planner agenda book once informed me, good writers know to begin with the end in mind, rather than making it up as you go along. It took me several years to finally accept that what they said was true; at least in most cases. Anybody can start making up a plot blindly, but unless you're already well-grounded in the way stories are supposed to be put together it can quickly run itself into a corner or become bogged down by challenges that weren't anticipated. That's one cause of dreaded "writer's block". When you know where the story must end up, it's not so hard to make it go there.
In fact, the more "plot points" are known beforehand the easier writing generally becomes, since it's easier to invent a plausible excuse for why something might happen a certain way than to realistically calculate the natural outcomes of non-existent people in non-existent settings, and then project them forward in time. Essentially, the author's job is to make these predetermined plot points seem true to life and inevitable in hindsight by adding and subtracting story factors until the chain of events withstands scrutiny, and carries the reader's attention. Simply deciding where to begin and end a story, or which parts of the story to show and which parts to ignore, proves that no matter what their creative process may involve, or how much it seems like they're allowing the story to unfold naturally, the author is the one controlling what you see.
Every element of a story is deliberate, serving a purpose in the narrative whether big or small. If it fails to serve a purpose, it's removed or changed. Solid Snake isn't addicted to cigarettes because it's logical, he smokes because it makes him seem tough, associates him with other famous hard-boiled anti-heroes who smoke, and warns children who want to imitate him that your proverbial "LIFE meter" will be depleted by doing so; and, of course, allows you to see the infrared beams if you don't have thermal vision goggles. The cigarettes fulfill these roles, and hence they exist in the first place. The cigarrettes would never be there just because — despite the sincere wishes of the creator — the logic of the story demands it. It won't be counterproductive, and to imagine that they even could be is to completely misunderstand the creative process.
To further break the illusion and reveal the creative process behind fiction, take a look at the deleted and alternate scenes on a DVD, or better yet listen to the commentary tracks. Nothing about it happens in a natural, straightforward way. The final scenes of a movie are often filmed first, just as the last chapters of books are often outlined long before the events which seem to lead up to it. The dirt and blood you see on the actor's faces in the final scene isn't even the same dirt and blood that got sprayed on them ten scenes prior — they had to be carefully painted on by a professional to make it look consistent. Once you hear the director talk about becoming frustrated with the uncooperative weather during the movie's filming, you really start to think about how phony and contrived it all is. We always know that it's fake, but it's not until you actually manage to watch the final product from the creator's perspective, and see all of the trickery involved, that you can appreciate it.
Frank Lloyd Wright doesn't see your house
Generally speaking, anybody who possesses some degree of expertise will be able to perceive things that the average person is ignorant to. When I start my car engine all I hear is a whirring, rumbling mixture of engine sounds, but the old mechanic hears a specific problem within moments, and can diagnose it without even opening the hood. His ears are tuned to sort out and evaluate everything; fuel injectors, carborators, spark plugs, et cetera. And, if you're better at something than those around you, you'll understand what it's like to see things with a trained eye too.
You don't have to be a highly paid professional or an official "expert" to know that behind everything we see there are tricks of the trade; secrets and unlockable knowledge hidden from the average person. How something is made — how to deconstruct it — is valuable knowledge that opens our eyes to a deeper level of understanding, no matter what it happens to involve. When famous architect Frank Lloyd Wright looks at your house, he doesn't see "your house"; he sees a structure that has beams, bricks, tiles, pipes, ducts, shingles, paint, plaster, nails, screws, and wires that all combine to create something that would be suitable for a human being to live in comfortably, and could be called a house if you wanted to call it that. He looks beyond the sentimentality of a bird's nest and sees instead the sticks and mud of which it is comprised. The same thing applies to writing and storytelling.
You can be the biggest fan of J.R.R. Tolkein's stories in the world, memorizing every detail of Middle Earth like a walking encyclopedia and taking part in costumed roleplaying events all around the world, and still not know anything about the narrative purpose behind why the One Ring must be destroyed in the fires of Mount Doom instead of a couple of miles down the road at the magic blacksmith's. Despite the entirely indisputable fact that the One Ring was forged by Lord Sauron out of supremely resilient material found in that hellish volcano—and therefore can only be destroyed by returning it to the same fires which melted the material in the first place—the storytelling mind knows that the real reason is because it makes for a really awesome story to force the characters to go to Mount Doom, and not down the street. It doesn't mean that story's internal logic is flawed, it just uncovers the unspoken purpose. To say that the real reason is actually the one given in the story, however, is to pretend that it's not all an illusion created by a man for his own reasons to begin with.
There's a mop blocking the elevator
I have one last aside to deal with before turning your attention to Metal Gear itself. If you're frothing at the mouth with anger at this point because I've been downplaying the wonderful, liberating nature of on-the-go story creation, or resent my generalizations about the creative process, or am doing too much to spoil the magic of fiction, then let me simply say that, in the case of videogames particularly, design is king. More than any other medium, videogames must have a tremendous amount of design emphasis (as opposed to creative sponteneity,) simply in order to work. Since the audience is not a mere observer following along with what you choose to show them, but an active ingredient who can explore and interact, contingencies must be accounted for, to the point where even the most insignificant dead-ends and back corners beg for the designer's attention. Designers know that players have an innate tendancy to explore the remotest areas of the "world" and bash their heads against the walls, no matter how much you tell them to focus on the objective. No matter how many deterrances and incentives you come up with for staying "on track", chances are they'll still take their sweet time looking around, until their curiosity is satisfied.
Invisible boundaries and cheap excuses must be used in order to make "unimportant" areas inaccessible, even though there's no logical reason for why they should be. How many times haven't you ran up to a doorway thinking you were about to to discover a new area, only to find that it's locked, unresponsive, painted onto the wall, or otherwise blocked by something silly that the character could easily navigate around? If a videogame was realistic, there would never be a boundary to a map. Some games at least have the decency to script a "I don't need to go here right now" message of some sort to make it official, but most are content to let the player jump, shoot, and scramble until they learn the hard way. Mini-maps, compasses, chattering support characters, color-coding, conspicuous shimmering effects, and many other design solutions have been created to solve the problem of the wandering player. Movies, on the other hand, never have this problem. In movies the characters only do what the director wants them to do.
It's because players love to push everything to its limits (often in the hopes of getting a secret reward for their persaverance!) that game designers must think about the psychological effect of everything they include. A novelist may think about what the reader's reaction will be when writing, but the game designer must think about how to anticipate and preempt your reactions in such a way as to guide you to where you must inevitably go. On some level it's the player who's being controlled by the designer, not the character by the player. If that sends a chill down your spine, try to relax and understand it from the designer's perspective: what else can they do? It's for your own enjoyment that they coax you into doing what you're supposed to. They know that beyond that wall you're trying so hard to jump over, there ain't no fun.