Is Lyanna Stark Jon Snow's mother?

Spoiler Alert!

If you have not yet seen the third episode in season six of Game of Thrones, then you are now warned that this post contains some details from it. The episode was called Oathbreaker, and the story was mainly about Jon Snow. Yes, he is alive!

For me the most interesting part of the episode was the scene where a young Eddard Stark fights against two members of The Kingsguard in front of a Dorne castle. This was towards the end of the war known as Robert’s Rebellion, and the mad king was dead. What was so important to protect, that two members of The Kingsguard needed to defend a castle in the far end of the realm, rather than stay in the capital with their king? As the sword fight progresses, it becomes clear to his son Brandon watching, that his father has lied to his children about how he defeated Ser Arthur Dayne. What else has he lie about?

This got me thinking about two stories in A Song of Ice and Fire (Game of Thrones) that I have always had my doubts about. The first one is the story about how Eddard Stark had an affair during the war that resulted in Jon Snow being born out of wedlock. Every time someone told the tale, the details were a little bit different. Was the mother a servant or noble woman? Was her name known or not? Was she dead or alive? If it was the latter, why did she not try to keep in contact?

The second story is how Robert’s Rebellion started. Eddard Stark’s sister Lyanna was enganged to Robert Baratheon when we was kidnapped and later killed by Crown Prince Rhaegar Targaryen. When Lyannas father Lord Rickard Stark (Warden of the North) and her elder brother Brandon Stark came to King’s Landing to protest about the kidnapping, The Mad King Aerys II Targaryen had them both killed. That got the houses of Baratheon, Stark, Tully and Arryn to rise up in rebellion. Despite the foul act of Rhaegar Targaryen, every one who knew him always spoke of him with the highest regard. Why did the perfect gentleman, the noblest knight, heir to the throne and a model man become such a villain?

Here is what I think happened

I do not think Eddard Stark was Jon Snow’s father. The only reason he lied about such an important matter that got to shape his life and cast a shadow over his marriage to Catelyn Stark was that the truth was much worse.

Rhaegar met Lyanna at the jousting tourney at Harrenhal. It is a known fact that he fancied her, and I think the feeling was mutual. Perhaps he did kidnap her, or perhaps they fled together. Nevertheless I think they fell in love. Does this sound familiar? Yes, it should, because it is pretty much how the story of Paris of Troy and the beautiful Helen goes in The Illiad by Homer.

After killing Ser Arthur Dayne, I believe the young Eddard Stark went into the castle only to find his sister Lyanna and her new born son that she got after the romance with Prince Rhaegar. I think she either died giving child birth, or perhaps Eddard Stark killed her because shame and anger when discovering that the whole rebellion was based on a lie. Then I think Eddard found the child, and decided to raise Jon as his own bastard. Both to honor his sister Lyanna, and also to atone for his sins in the war.

So..what do you think? Is Jon Snow the first heir to the throne of The Seven Kingdoms? Is he half Stark and half Targaryen? Will he marry Daenerys? Afterall, the Targaryens have a tradition of marrying their siblings J