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I understand that the main quest can be completed without taking sides in the civil war, but I'm at the point where I'm contemplating finishing the main story line. I'd like to go back and do the civil war afterwards. Has anyone done that successfully?

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Haven't tried, but seeing how every major questline was independant from another (i.e. killing the Emperor doesn't affect Imperial Legion (Civil War) questline) I'd say you can finish <whatever you want> then start <something else> safely –  Evgeni Jan 17 '12 at 20:34
    
This is my hope. There have been some very specific bugs about quest completion, so I'm a little scared of losing out on such a big quest. Then again, I don't want to get bugged out of completing the main story line for some reason either, so I'm going forward with that one! –  Bob Jan 17 '12 at 21:16
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up vote 10 down vote accepted

Yes.

I've done this succesfully. The main questline was one of the first questlines that I finished (mainly to get the Dragon Shouts exclusive to it), and the Civil War questline (the Imperial Legion path) was one of the last questlines I finished (because I can't decide who to support, initially).

A word of warning, though: There are a few bugs associated with one of the main quests, coming from a variety of questlines, including the Civil War questline.

If you do not trigger these bugs, or have done a workaround, you should be able to complete the Civil War questline even after the main questline has been finished.

More info:
http://uesp.net/wiki/Skyrim:Main_Quest
http://uesp.net/wiki/Skyrim:Stormcloaks
http://uesp.net/wiki/Skyrim:Imperial_Legion

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Thanks for the Season_Unending quest bug list. –  Bob Jan 18 '12 at 15:09
    
You missed mentioning the Battle for Whiterun bug regarding Heimskr's house. –  Iszi Jan 18 '12 at 23:09
    
@Iszi Is it this bug? Could you explain how it will affect completion of the Civil War questline after the Main questline has been finished? –  galacticninja Jan 20 '12 at 3:47
    
@galacticninja Ah, I see what you were doing now. As far as I know, Battle for Whiterun does not have any bugs that affect the Civil War questline after completion of the main quest. I would still note that this, and the rest of the Civil War questline for that matter, does have bugs that can affect other questlines. If you want to be a completionist, leave the Civil War questline as far at the bottom of your to-do list as you can. –  Iszi Jan 20 '12 at 15:02
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The thing is, you have to do part of the main quest lines in order to do the civil war quest line, because the Yarl of Whiterun won't pledge allegiance with the Imperials until you go into Bleak Falls Barrow and retrieve the dragon stone for his court wizard. I imagine if you do the civil war quest line before you finish the main quest line, the peace meeting the gray beards put on might not happen (haven't tried it) because in the civil war quest you

kill Ulfric (as an imperial soldier) or kill General Tullius (as a storm cloak), both of which are at the peace meeting.

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Dude, spoilers. Anyone asking about this hasn't got to that part of the game yet! –  SevenSidedDie May 9 '13 at 14:52
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