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If the civil war is still going on in Skyrim when you reach the main quest
, then the Jarl of Whiterun will tell you that he won't allow you to use Dragonsreach to capture a dragon until he doesn't have to worry about his city being attacked. You'll then have three ways to proceed:
- You can side with the Imperials (by talking to Tullius and Rikke in Castle Dour in Solitude) and complete their quests, which will cause the Imperials to win the war.
- You can side with the Stormcloaks (by talking to Ulfric and Galmar in the Palace of the Kings in Windhelm) and complete their quests, which will cause the Stormcloaks to win the war.
- You can convince the Greybeards (in High Hrothgar) to host a peace treaty, which will allow you to put the war on hold until you've dealt with Alduin.
The first two options are covered in the quest lines for the Imperials and Stormcloaks. For the latter option, you'll need to do a lot of traveling and talking. First you'll need to talk to Arngeir (in High Hrothgar). Reluctantly, he'll agree to host a summit meeting. Next you'll need to talk to General Tullius (in Castle Dour in Solitude) and Ulfric Stormcloak (in the Palace of the Kings in Windhelm) and convince them to attend the meeting. No matter what you say to them, they'll agree to come.
After setting up the meeting, when you return to High Hrothgar, you'll find everybody there, including Esbern and Delphine. To get the meeting started, you'll need to talk to Arngeir (near the entrance) and then take your seat at the council table (in the eastern part of the building).
For the negotiations, you'll be named the arbiter. No matter what you say, or how one-sided your decisions are, both sides will eventually agree to the terms, with the only consequence being that some jarls will get replaced. If you previously joined the Stormcloaks or the Legion, and if your faction comes out ahead in the negotiations, then you'll receive a random enchanted weapon at the end. Otherwise, you won't receive anything.
Note: At the end of the negotiations, Delphine will come up to you, and she'll give you the quest
, assuming you didn't receive it earlier.