14 years prior to the events of A Game of Thrones, one of Westeros most defining conflicts ensued, resulting from the apparent kidnap of Lyanna Stark (who was at that time betrothed to Lord Robert Baratheon) by the heir to the Iron Throne of Westeros- Rhaegar Targaryen. One year prior to this apparent abduction, at the Tourney of Harrenhal, Rhaegar had emerged victorious after unhorsing esteemed fighters Brandon Stark and Ser Baristan Selmy in the jousts. The tourney had been the most extravagant that Westeros had ever witnessed, and most notable members of the Realm had turned out in force.
In a shock culmination to the tourney, Rhaegar had selected Lyanna Stark as the Queen of Love and Beauty by gifting her with a crown of blue winter roses. Such an act was considered outrageous by the attendant nobles because, in choosing Lyanna, Rhaegar had not only overlooked his own wife, Elia of Dorne, but also gravely insulted House Baratheon- since Lyanna was betrothed to be married to Robert Baratheon at this time.
After the suspected seizure of Lyanna, her brother Brandon Stark- elder brother of Ned and at that time heir to Winterfell and the North- rode to the Red Keep at Kings Landing and, in a scene that recalls Achilles screaming for Hector to come forth at Troy, demanded that Rhaegar come out to face his doom. King Aerys II Targaryen, slowly succumbing to the increased paranoia and ravages of insanity that had characterised the lives of many of the pure-bred Targaryens, imprisoned Brandon and his entourage for conspiring to murder the Crown Prince, and demanded that their fathers march south to answer for the sins of their heirs. Brandon was then forced to watch his father die with a noose around his own neck and a sword just out of his reach. When goaded to try to reach the sword to save his father Brandon only succeeded in strangling himself to death.
The Mad King, not content that the scales of justice had been balanced, then demanded the heads of Robert Baratheon and Eddard Stark from their guardian- Jon Arryn, Lord of the Eyrie. Disgusted at the injustice and at Arys increasingly fragile grip on reality, Lord Arryn had raised his banners in revolt and declared war in allegiance with House Baratheon and House Stark. Before marching to aid Robert, who was warring in the south, Ned married Catelyn Tully, who had previously been betrothed to his brother Brandon before his death at the hands of the Targaryens.
We are led to believe that sometime during Roberts Rebellion (or The War of the Usurper, depending on which side your sympathies lie) Ned Stark, now Lord of Winterfell, cheated on his wife and fostered a bastard child that he brought back from the war. That child was Jon Snow.
Now youve been reacquainted with the background, lets discuss the clues about Jons true origins