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Since the people who made STALKER have no idea how to do proper quest triggers, the Strelok's Flash Drive quest (Which is required for the best ending) only completes if you exit through the manhole in the base, as mentioned before. When I played, I got it, backtracked, came out the way I came in, and did some awesome commando stuff to infiltrate the military base. In order to get the good ending, you have to go down into the Agroprom Underground, get Strelok's flash drive or whatever, and then exit through the manhole in the Agroprom base.
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