In System Shock 2, I’ve escaped both spaceships, the Von Braun and the Rickenbacker, and have gone into the mind-hive of the Many to fight them. There must have been something in the air in ’99, because the endgame of System Shock 2 feels a lot like the endgame of Half-Life, down to the shooting-the-stars-around-somethings-head-and-then-exploding-it.
There’s a certain logic to it, to some extent. It’s easier to render indoor environments than outdoor ones, because a man-made environment is far less complex and more familiar. Therefore, SS2 is set in a spaceship, Half-Life in a research facility. When things need shaken up for the endgame, it only makes sense to switch from inorganic to organic, but not to real organic, because the rendering capabilities weren’t up to that. Thus, you get Gordon Freeman from Half-Life jumping a portal into parallel universe Xen where everything is neon green and squishy-soft, and my Space Navy Guy heading into the red and gooey mind-hive of the Many (which isn’t the actual end of the game, but it’s pretty close.)
From other angles, however, this is a bad move for a video game, mostly because a game shouldn’t be playing to its weaknesses in the last couple of levels. If you’re going to put something technically experimental in a game that you’re not sure you’ll be able to pull off, it’s best to do it somewhere in the middle: If it’s at the beginning, it’ll drive people off; if it’s at the end, it leaves a bad taste in their mouth. In their native angular environments, SS2 and Half-Life look remarkably good even ten years later (SS2 only with a bit of modding), but when you move to the organic places, it’s just ugly and difficult to get around in.
So why do they do it? I’ve mentioned one reason above, but as far as I can tell there’s another reason that’s more fundamental to games and gaming culture. Partly because of their history as computer/console artifacts, and because of their mode of combat, shooters have always to some extent been about the (good) machine-like versus the (evil or weak) biological.
The body in most of the shooters I’ve played is envisioned as machine-like, technological, and mathematical. Sometimes this is literal, like when you’re a scientist in Half-Life or a mechanically-enhanced soldier in Deus Ex or Crysis or Lost Planet, for that matter, also Half-Life. In many other cases it’s metaphorical; you represent part of a crack team of soldiers who, when together, function like a machine (Call of Duty, F.E.A.R.) or a fighter designed to restore order (Resident Evil 5.)
You’re rarely, however, fighting a force that’s like you. There’s an important gameplay reason for this (re: drones are boring), but it’s also that fear and horror in a game is evoked through the hideously biological or unscientific. In Doom this is demons and Hellbeasts in space: Religion and atavism are invading the scientific domain of the space exploration project. In Lost Planet it’s a giant bug that keeps getting in the way of your terraforming, so you fight it in a giant robot suit. And so on.
Half-Life decided to consciously take this to extremes, so you’re basically a tidy physicist fighting messy biology. Your enemies (the Gonarch–a combination of gonad and monarch–the headcrab, a jumping vagina dentata, and the Nihilanth, a giant fetus in a stone-rimmed womb) are alien, but evoke human sexuality (this was referred to in Raising the Bar, Valve’s book on developing the Half-Life saga, as a way to exploit the “inherent homophobia of 14-year-old boys.”)
When you’ve built your game around this, an organic endgame is vital, because flesh has become the most terrifying thing a person can face. After all the developments of engineering and physics in the twentieth century (and the space program and computing really did make it the century of physics) the flesh is the one thing that is seen as sacrosanct and unchangeable, but also the source of our destruction. To change the flesh is frightening–hence our fear of body-snatching and cyborgs–but in the end, the flesh will decay or tumesce. The flesh will betray you, no matter how many guns you have. You are going to age and die. And shooting as many external reminders of that as you can is all you can really do about it.
P.S. Bioshock is really interesting in the context of this and Susan Faludi’s Backlash. I’ll have to talk about it sometime.