Well, R+L=J. It’s pretty clear. Timeline-wise, we learned a lot from WOIAF.

Rhaegar and Lyanna disappeared very close to the Tourney at Harrenhal – around 2-3 months close. Lyanna was in the area of the Gods Eye to be “abducted” because she was, in all likelihood, staying at Riverrun prepping for her brother’s wedding. Note that this timing almost certainly excludes Brandon from being Jon’s father, and probably excludes Ashara from being Jon’s mother with either Stark. 

Here’s what I think happened with Ned and Ashara – I think the two of them fell for each other and hooked up at Harrenhal (Ser Barristan wasn’t at the tent at the time and probably jumped to the same conclusion that much of the fandom did, given Brandon’s rep). At the time, as Harwin points out, both of them were unmarried and a fairly good match – he was the second son of a Great House, she was the daughter of a Lesser House and no heiress. They probably hoped that they would get married shortly, and I wouldn’t be surprised if they were actually betrothed or in the process of becoming betrothed.

And then things went to shit. Lyanna disappears, Brandon hulks out, Elia’s abandoned by her husband, then Brandon’s arrested, Rickard shows up for the trial, and both of them are dead. Suddenly, Eddard is a rebel on the run for his life and Ashara is trapped on the other side, torn between her loyalty to Elia and her love for Ned. 

At some point in this process, a few things happen, and I’m not sure in what precise order they happen: 

• Ashara Dayne is sent home when she begins to show.
• Ned returns to the South at the head of an army.
• Elia and her children are taken from Dragonstone to Storm’s End. This must have happened after Ashara is sent away, because Ashara is not in King’s Landing during the Sack.
• Rhaegar reappears with the Dornish troops.  
• Arthur Dayne reaches out to his sister for help with Lyanna’s pregnancy, and Wylla, a longtime retainer at Starfall, is sent to the Tower of Joy as midwife and nursemaid. 
• Ned and Ashara meet for the penultimate time, Ned finds out where Lyanna has been hidden. 
• Ned is told that he has to marry Catelyn Tully in order to fulfill the pact made by his father and keep the rebel alliance intact, and does so. 
• Ashara, now forsaken by Ned and carrying a bastard instead of a euphemistically-premature trueborn child, suffers a miscarriage. 

Then comes the Trident, the Sack, and the lifting of the Siege of Storm’s End. His duty to Robert fulfilled, Ned is free to ride full-tilt for the Tower of Joy. He arrives, and he and his companions fight Ser Arthur Dayne, Ser Gerold Hightower, and Ser Oswell Whent. Only Ned, Howland Reed, and the servants (including Wylla) are left alive.

Ned takes Dawn back to Starfall and meets Ashara for the last time. The two of them are wracked with grief – for a lost child, for her brother, for his brother and sister and father, for the life together they cannot have. The pain and the guilt are too much for Ashara to bear, and she kills herself. 

Ned remains at Starfall – rather than blaming him, the Daynes recognize his honor, their mutual loss, and the cruelty of fate – until Jon is ready to depart. The Daynes agree to keep his secret, and help spread the story that Jon is Wylla’s son, a story that Ned repeats to Robert in King’s Landing, and probably spreads on his boat-ride back to Winterfell via the Three Sisters. 

Ned and Catelyn’s marriage, already a rocky start in which both are forced to put their family’s interests above their own personal desires, is further strained by Ned’s cover story.