I found this confusing too, the time line seems very messed up for Great War(His torture) > Markarth incident(Him being betrayed > Start of the rebellion somewhere in between there is meant to be the last straw of the banning of Talos, which I'd have figured to be the end of the War but maybe it was a recent addenum made by the AD. I found characters seem to refer to the rebellion as both old and new, Imperials were there anyway or they just arrived to fix a troubled area. I can't even work out how long ago the killing of the king was or if the hunt for Ulfric started as soon as he fled or a while after. Plus why Darkwater pass and why are we going to helgen on a road that only leads to out of skyrim?
Frankly it comes across as poorly plotted out, guess we'll have to wait til TES VI for an ingame book that talks about it all.

The Great War ended some 26 years before game time.  During this time, Ulfric was starting to agitate for independence from the empire.  A few years before game time, the imperials who had been kicked out of the Reach by the Forsworn (when the legion pulled out of that area to go fight in Cyrodiil) asked Ulfric to go in and retake Markarth and in exchange they would be allowed to worship Talos freely in that city.  He did it, but the Thalmor found out and the imperials threw Ulfric under the bus and imprisoned him.  During this time, Ulfric's father, the jarl of Windhelm, dies.  Once Ulfric is released from prison, he returns home, becomes jarl and challenges Torygg to a duel, beginning the Stormcloak rebellion in earnest.  Half the country give or take joins him by game time.  Darkwater Crossing is a Stormcloak area, so they thought they were in safe territory when they were ambushed.