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What happens if I clear a dungeon before receiving instruction to do so?

For an example, the Valtheim tower usually is a place where we hunt a bandit based on an bounty letter instructions. I "mistakenly" cleared the area before obtaining the bounty instruction. Can someone explain to me what happen in that case? I'm afraid that i might have aligned or "destroyed" the story, if you get what I mean. Need help! Thanks!

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If I recall, in most cases there's a beef gate that makes it very difficult to do so. But in cases when you overcome the beef gate, the game doesn't handle it very well. – Ataraxia Aug 6 '13 at 4:55
@Zetta I've never actually seen that in Skyrim; could you provide an example of what you're referring to? – Emrakul Aug 6 '13 at 4:56
@Emrakul Most of the times I have noticed that when you enter a dungeon that you're not chronologically "supposed" to go in, the enemies are leveled at points appropriate to what you what level you're expected to be at. Going to High Hrothgar, for example, you encounter at least one frost troll. – Ataraxia Aug 6 '13 at 5:46
@Zetta That frost troll is there regardless of whether or not you're supposed to go to Hrothgar. – Emrakul Aug 6 '13 at 5:47
@Emrakul I don't recall ever saying that it wasn't... – Ataraxia Aug 6 '13 at 12:42

No, it appears to have no effect in most places. While there is no official documentation about the prevalence of these bugs, Skyrim is known to have several imperfections which have not been accommodated for in quality assurance and testing.

In other words, use caution.

More specifically, all clearing a dungeon does is raise the respawn time for that dungeon from 10 to 30 days. After the respawn time, people and plants, etc. will return, but not special items. There are certain dungeons which do have an impact on plot, though; most notably are the dungeons which typically contain Hrolfdir's Shield. If you clear those, you are stuck in the questline, and need to use the console to get around it.

Most of the time, things will just come back. But, some of the time, if a dungeon is particularly significant or impactful, something might break. Bear this in mind, and crawl wisely! Some dungeons will have a general impact on the game. The best advice I have is to not think about spoiling dungeons, and just enjoy the game.

In your specific case case: I have reason to believe that the units in Valtheim will be back in 30 game days, and you will then be able to complete the quest.

Source 1, Source 2. See: Radiant storytelling.

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Wow, your answer really calms me. You provided many important insights as well. Thanks a lot, Emrakul! The thing is I was just wandering off then I see this huge tower and I wanted to check that place out. Suddenly there were some bandits attacking me, and well, one thing leads to another and I realized that I killed a bandit leader. At that time I had already saved the game and I dont have a backup. So anyhoo, in my case, I shouldnt be worried about it then ya? Thanks again brother! – Pontius Aug 6 '13 at 5:37
@Pontius Probably not. You can relax on this one :] It happens. – Emrakul Aug 6 '13 at 5:38
Nice answer. +1 – ヴァイシャリ Aug 6 '13 at 7:51
@Emrakul your name is win – Ender Aug 6 '13 at 14:23

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