Okay, I'm walking through it for the fourth time, and it struck me: this is great for guys who play so they can pretend to sneak up on people and cut their throats, beat them to death, and shoot them in the face. But if this was IRL, it doesn't make strategic sense.
Joel's goal isn't to kill bad people—and don't get me wrong, those people richly deserve it. But he's trying to move Ellie across the country. Obvioulsy, I would think, he should bypass buildings full of armed gangs (including gamgs of cops). He should sneak ellie past the building or at worst, tiptoe through the basement.
Back in Boston, okay. You had to be indoors or you were a target for the military on the street.
And when Joel shoots up the hospital at the end, hell yeah! He is driven to rescue Ellie without regard to if he gets killed. Watching the development of that mutual dedication is why I do this over and over.
But even in suburbs and semi-rural areas where he could bypass trouble, Joel shoots and stabs and molotoffs his way through the middle of town. (The wonderful Bill chapter was an exception!)

This isn't his goal. It's to get Ellie to Tommy's and save humanity.
But doing that puts Ellie (and therefore humanity) in terrible risk.
Even if she manages to dodge all the bullets, if Joel gets killed, she will never find Tommy and the fireflies on her own. Joel staying alive is as important to saving the world as protecting Ellie.
I believe Neil said that he wished he didn't have to force-fit in all these battles so he could just tell the story, but he had to or no one would play it. Wish I had a link.
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I'm pretty sure it's a stupid question, particularly to people who play because setting strangers on fire and watching them scream is rewarding all by itself—not just a necessary and very dangerous task required to cure the fungus. But my question is, does all of this death mission trouble-seeking make some kind of goal-directed, logical sense in the game universe that I'm missing?
Or is the story obviously just a thin excuse to kill simulated people, and I'm being characteristically naive and childlike for not just knowing that automatically?
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I'm sorry this is too long, but I have to be explicit about what I'm saying—particularly in my first real post—because stuff I say at other places is often met with "U dissin the gamerz communtiy, bitch? It's a FPS. Go back to tea partys in second life!" I eventually just say "fuck it" and try again to find somewhere that the commenters aren't fucked up and take everything I say as a personal attack on their weak, desperate egos. I chose here specifically because from reading posts, you guys seem to be thoughtful and not just mindlessly hostile teenage game bois.