So...
THE DARK BROTHERHOOD
All is going well when the legion attacks and clears out the whole sanctuary killing EVERYONE
You then have to go KILL CICERO
Cicero was the ADORING FAN!!!!!!!!!!!!!!!11111
The THIEVE'S GUILD
The main guy steals everything from the guild and you have to KILL HIM
THE COMPANIONS
You become a warewolf
You kill warewolf hunters
The leader dies and you become the leader (Shocker, AMIRITE)
MAGE'S GUILD
The obvious THALMAR badguy turns out to be the bad guy and you kill him.
MAIN QUEST
You kill dragons and get shouts
You have to kill the leader of the bad dragons
to do this you capture a dragon and ride on its back to heaven ( FOR REALS )
You kill the badguy with some help from some other people who can shout
Oh and there may have been some mentioned spoilers in the text above...
Now that you know what happens you can proceed with the rest of your life.