Who is Jon Snow's Mother?

Jon Snow's mother is mentioned rarely by Eddard Stark. She is a subject of mystery to everyone except for Eddard Stark himself. It is in my personal belief that Jon Snow's mother is in fact Lyanna Stark, and that his father is Rhaegar Targaryan.

The evidence of this is in the story of the war that took the Targaryans from power and Robert claimed the throne. Robert was in love with Lyanna Stark. The war started because Rhaegar came upon Lyanna and stole her away. "...Rhaegar fell upon Lyanna Stark of Winterfell, and carried her off..." (World of Ice & Fire, 127). He held her captive for almost a year, until Eddard finally came to High Garden where he fought Rahegar while Lyanna could be heard screaming in the distance.

The second bit of evidence is while Danaerys is in the house of the Undying Ones in Quarth. She see's a series of visions of her family long dead. She see's Rahegar in a room with his Dornish wife and their two children saying: "'There must be one more...The dragon has three heads." (Clash of Kings, 701). Much later she see's a blue rose blooming on a wall of ice, providing a sweet scent to the area.

Rhaegar desired to have three children, and his wife was incapable of having any more after their second child. Rhaegar, like most Targaryans, was obsessed with the glorified stories of his ancestors and their dragons. He wanted to relive those days, including the old tradition of threes that runs in his family. There are three heads on the dragon on the Targaryan banner. Rhaegar no doubt also observed that his ancestors could have multiple wives, and so he desired to marry Lyanna Stark, but custom would not permit it. Rhaegar formed designs around Lyanna since at least the great Tournament at Harrenhall: "And when the triumphant Prince of Dragonstone named Lyanna Stark..the queen of love and beauty...thus given insult to his own wife, the Princess Elia Martell of Dorne..." (World of Ice & Fire, 126).  So he swept her off, married her, and they conceived Jon.  A year after her abduction Lyanna was giving birth when Eddard Stark was coming to her rescue. When she see's her brother, she knows Robert's forces have won. She knows that Robert means to kill all Targaryans. She may have been raped but she still loved her baby, so she asked Eddard to claim him as a bastard. "Promise me Ed." No Targaryan must survive this rebellion and no Targaryan did, only a Stark left that tower. And given the fact that Robert's blood lust for Targaryans never departs him while he lives, Jon, Catelyn, nor anyone could be told of Jon's true identity. Eddard may have lied about who Jon is, but when has Eddard ever put honor before his family.

The blue flower in the wall of ice that Dany saw in the house of the Undying Ones was a symbol of Jon, who at the time was sworn to the Night's Watch. "A blue flower grew from a chink in a wall of ice, and filled the air with sweetness." (Clash of Kings, 706). It is difficult to tell whether this moment in the house of the Undying was a vision of the present or a vision of the future. This may give the reader hope that Jon will survive and thrive at the wall. The blue flower was meant to reference Lyanna Stark, who is known to have loved winter roses.

Jon's parentage may never be concretely spoken, but there are these hints laid throughout the story to hopeful direct the reader towards the truth. It lends power to the mystery of Jon Snow, and if this is true it adds to his regality of character. As well as some unease, for when a Targaryan is born a coin is flipped: on one side is greatness and the other side insanity. It appears from Jon's success at maintaining the wall and becoming Lord Commander he his coin landed on the side of greatness.