Total Nerd Clues That Point to Jon Snow Being a Targaryen  

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We’re giving birth to SPOILERS in this list! 
 
If you are a book reader from the way back, the Ned Stark bastard Jon Snow question has been speculated upon for a couple of decades. Why is it important that we know who Jon really is? Because it will have a large impact on the story overall. In the Game of Thrones storyline, It’s go time and the White Walkers are coming, bringing the threat of a Long Night and the destruction of men with them. We’re going to need some real heat, fire, and magic. If Jon Snow is actually a Stark and a Targaryen, he may just be the Azor Ahai we’re looking for. 
 
If Jon is the son of Lyanna Stark and Rhaegar Targaryen, he is Daenerys’s nephew - if you believe that Dany’s parents are Aerys and his sister/wife Rhaella. If you are in the "is Jon Snow Daenerys’s brother?" camp, then you believe that Dany and Jon are the children of Lyanna Stark and Rhaegar Targaryen. Ned brought Jon with him to Winterfell with the ruse that Jon is his bastard with a lady he knew during the war because Jon favored the Starks in appearance and Dany was ferreted far away because it was obvious she looked like a Targaryen. You buying it? Some say it’s too easy and that Martin doesn’t write that way. But consider this…
 
Targaryens go together like Tyrion and brothels and the Song of Ice and Fire will really take off when we add Jon to the trio fans speculate will become the Targaryen dragon riders. As the characters come together, they will surely make a mightier force than if they are kept apart. Throw in the theory that Tyrion Lannister is also a Targaryen and then we’re closer to the three-headed dragon prophecy that has the three Targaryens riding on the backs of Drogon, Rhaegal, and Viserion to restore order to the Seven Kingdoms and quell the White Walker invasion beyond the Wall and probably bomb Cersei’s house just for good measure. 
 
It would be rather satisfying to finally answer one of the biggest Jon Snow theories in this universe since we finally got to the bottom of Kit Harington’s season six resurrection bob. Now that his watch has ended and he no longer needs a big hairy Lord Commander coat, hopefully we’ll see Jon make his way to Dany and Tyrion with a stop over at Winterfell to kill the crap out of Ramsay and free Rickon and Osha/Tonks and avenge Shaggydog. RIP Shaggydog. 
 
At the very least, we should get the answers to the questions of "who is Jon Snow’s mom?" and "is Jon Snow a Targaryen?" It looks like we’re about to find out if R+L=J is true and if that’s the case, well, Catelyn/Lady Stoneheart owes Jon an apology. And all of those other dudes who have been calling him a bastard with relish all these years need to send respect ravens. Also, bye Olly! 

The Presence of the Kingsguard at the Tower of Joy


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By the time Ned tracks down his sister Lyanna at the Tower of Joy in the Red Mountains of Dorne, Rhaegar has been killed by Robert. Before he can go to his sister in the tower, Eddard, Howland Reed, and his men (Lord William Dustin, Ethan Glover, Martyn Cassel, Theo Wull, and Ser Mark Ryswell) must face off with the Kingsguard Ser Arther Dayne, Ser Gerold Hightower, and Ser Oswell Whent. Chris Holden points out that this is “curious” because there were no royals present, unless Lyanna is carrying Rhaegar’s paper, a lineage the Kingsguard are sworn to protect. 

Maester Aemon and Jon, Targaryens at the Wall


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Jon learns that Maester Aemon is actually Aemon Targaryen. They have a talk about choices, duty, and temptation as Maester Aemon talks about the day the ravens brought news of the decimation of his family, but all we heard was the roar of foreshadowing.

Also, in a scene where the maester talks with Sam and a raven concerning Dany, the maester says, “And she’s alone. Under siege. No family to guide her or protect her. Her last relation thousands of miles away. Useless. Dying. A Targaryen alone in the world is a terrible thing.” And then Jon Snow walks in the room and asks for guidance from the maester. The maester tells Jon to “kill the boy and let the man be born.” Soon after Maester Aemon passes away, Sam leaves for Oldtown with Gilly, and Jon is stabbed by Alliser Thorne and Olly and other crows.

The maester’s words foreshadow Jon’s fate at the hands of his Night’s Watch brothers and his resurrection. Maester Aemon’s words could also foreshadow that the Targaryens need to be reunited in this world. 

Bran Is a Key to Jon’s Identity


Bran Is a Key to Jon’s Identit... is listed (or ranked) 3 on the list Clues That Point to Jon Snow Being a Targaryen
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This is rather obvious by now, but back in the beginning, there were hints that Bran would come to discover Jon’s true parents and aid him in his battle against the coming White Walker war. When he was younger, Bran was already on the path to Jon’s identity and importance. "I dreamed about the crow last night. The one with three eyes. He flew into my bedchamber and told me to come with him, so I did. We went down to the crypts. Father was there, and we talked. He was sad... It was something to do about Jon, I think." 

In season six, Bran wargs ever closer to the truth of Jon’s birth and will have a large role to play in the coming war, possibly by his cousin's side. 

Littlefinger Knows That Rhaegar and Lyanna Loved Each Other


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It’s Littlefinger’s job to know things and to not share them unless it serves his purposes. That scene in the crypt at Winterfell between Peturr Baelish and Sansa is telling. Littlefinger recounts to Sansa about the tourney at Harrenhal and how Rhaegar rode right past his wife Elia Martell to lay a wreath of blue roses the color of winter frost in Lyanna's lap. He marvels at how many men had to die because Rhaegar chose her.

Sansa balks at the word “chose” and says bitterly, “Yes, he chose her and then he kidnapped and raped her.” Baelish looks at her with a strange and knowing smile and responds, “Let’s speak somewhere the dead can’t hear us.” Maybe Littlefinger knows that the relationship was mutual and the subsequent child from their union is Jon. No need to share that news now, right?