Quick Answer: Since Game of Thrones' first episode, we've been uncertain as to the true identity of Jon Snow's mother. Now in its sixth season, it seems as though Ned Stark may not be Jon's real father. According to the popular fan theory R+L=J, Jon's actual father is Rhaegar Targaryen and his mother is Lyanna Stark. If this theory is true, that would make Jon a Targaryen, and therefore heir to the Iron Throne. What's more, it would make him Daenerys Targaryen's nephew.
In its first episode, Game of Thrones (2011 - ) posed a question that has yet to be answered: Who is Jon Snow's mother?
In Season 1, Episode 2, "The Kingsroad," Ned tells King Robert that Jon's mother was a woman named Wylla. Ned provides no further explanation, nor does he confirm whether or not Wylla is still alive. As the seasons go on, it becomes very doubtful that Jon's mother is a random woman. Not only that, but the true identity of Jon's father comes into question as well. Many fan theories have developed in order to get to the bottom of Jon's parentage, some extremely far-fetched. The most likely theory is one that most Game of Thrones fans should be acquainted with: R+L=J. In the equation, "R" stands for Rhaegar Targaryen, eldest son of the Mad King, brother to Daenerys, Prince of Westeros and heir to the Throne. The "L" stands for none other than Lyanna Stark, Lord Eddard Stark's sister. Based on what we know about the Game of Thrones timeline and its web of characters, the R+L=J theory isn't just plausible; it is nearly definite. Let's break down why this theory makes sense.
Cordelia Hill as Young Lyanna Stark in Game of Thrones
Prince Rhaegar was an extremely handsome man, and as a Prince, was desired by many. Tywin Lannister even hoped that Rhaegar would marry his daughter, Cersei. But the Mad King took the idea as a great insult, and so Rhaegar married Elia Martell of Dorne, sister to Oberyn Martell, in an arranged marriage. Later, at a tourney at Harrenhal, Rhaegar wins the joust, defeating Ser Arthur Dayne, the Sword of the Morning. Awarded with the crown of winter roses, a symbol of love and beauty, Rhaegar has the opportunity to give it to any woman he wishes. The obvious choice would have been his wife, Elia. But he walks past her and gives the crown to Lyanna Stark, whose favourite flower happened to be blue winter roses.
As the story goes, Rhaegar later kidnaps Lyanna for unknown reasons, ultimately triggering Robert's rebellion and causing him to win the Iron Throne. However, we don't know if Lyanna was truly kidnapped. It is entirely possible that the pair fell in love and ran away together. Given Rhaegar's character, this scenario seems far more likely. From what we know about Rhaegar, he doesn't seem the type to kidnap someone. He was said to be a kind man who much preferred playing music in the streets to fighting and killing, even though he had proven to be quite adept at the latter. It would be a lapse in character for Rhaegar to do something so vile as to abduct a person. In any case, whether by choice or force, we know that Lyanna disappears with Rhaegar. It should be added that this all takes place at the same time that Ned goes off to war and is alllegedly unfaithful, resulting in the birth of his bastard son, Jon.
Robert Aramayo as Young Ned Stark
When Rhaegar goes to fight the Battle of the Trident, the battle where he would fall and Robert would rise victorious, Lyanna is kept at the Tower of Joy, a scene we saw in Season 6, Episode 3. When Ned enters the tower, he finds his sister in bed, blood-soaked and dying. As mentioned, Rhaegar is not a character who's defined by his bloodlust. Therefore it is unlikely that he killed Lyanna. What's more, it's said that Rhaegar died with Lyanna's name on his lips, suggesting that the couple was very much in love.
There is, of course, another explanation as to why Lyanna was bathed in blood: childbirth. That would also explain the shrieks that Ned heard coming from within the tower. If this was the case, Lyanna knew that her child would not be safe. Being the son of Rhaeger Targaryen, the baby would be murdered immediately. Even if the child somehow survived his parents, who would take care of him? Lyanna likely would have asked Ned, her brother, to look after this child, even to raise him as his own. Ned, known for his honor and loyalty, would have agreed. He would come back from the war to his new wife, Catelyn, with a new baby in tow and admit that he was unfaithful. He would suffer the consequences of that for years to come, as would the baby. But the child would grow up, and no one would but Ned would know the truth of the child's parentage. He'd grow up a bastard, but at least he'd grow up at all. "J," therefore, stands for Jon Snow.
Kit Harington as Jon Snow
The truth is, Rhaegar and Lyanna were probably in love. Robert assumed otherwise because of his love for Ned's sister, and the rumors of his vicious kidnapping spread like wildfire. But more likely, Lyanna was never kidnapped or beaten. She ran away with the man she loved, she had a child, and died in childbirth. Ned honored his sister's wishes, raising Jon as a bastard and keeping the truth hidden for all these years. The timeline and story makes sense, and it all fits. There's a reason that R+L=J is one of the most widely believed and supported fan theories.
In an extension of the R+L=J theory, some fans also speculate that Jon Snow -- otherwise known as Jon Targaryen -- could meet and marry Daenerys. As Daenerys is Rhaegar's sister, that would make her Jon's aunt. Considering that the Targaryens often marry family members, a possible marriage between Jon and Daenerys isn't out of the question. Should this ever happen, the couple could rule Westeros together, and Jon could become one of the Dragon Riders.
What do you think? Is Jon the son of Rhaegar Targaryen and Lyanna Stark?