It was six seasons in the making, but on Sunday's Season 6 finale of Game of Thrones, Jon Snow's mother was finally revealed. But part of the R+L=J theory points to Rhaegar Targaryen as Jon's birth father. That's right, he's a Targ, so how are Jon Snow and Daenerys related on Game of Thrones? Until now, the only other Targaryens we've seen on the show were Viserys, Dany's big brother, and Aemon Targaryen, who was both their great-uncle and the maester of the Night's Watch. But true to Game of Thrones' characters having no plot armor in the earlier seasons, both are now dead, leaving Daenerys as the only living Targaryen that we knew of for sure until now.
As the R+L=J theory goes, Lyanna, Ned Stark's sister, ran away with Rhaegar Targaryen, Dany's much older brother whom she never even met. Robert Baratheon, who was arranged to be married to Lyanna, ended up leading Robert's Rebellion on the Targaryen house as a whole, certain that Rhaegar actually kidnapped Lyanna against her will. But instead of Ned finding Lyanna at the Tower of Joy, hurt or being tortured by Rhaegar, he found her just minutes after she'd given birth to a boy she would make Ned promise to raise as his own because, as she whispered to him, "If Robert finds out, he'll kill him, you know he will Ned. Promise me you'll protect him."
So if Rhaegar was Dany's brother and Lyanna's lover (or even husband, since that's still a decently grey area), how are Jon and Daenerys related on Game of Thrones? This new reveal of his true parentage proves that Jon is Dany's nephew and a rightful Targaryen himself. And, as fate would have it, the only other living Targaryen that we know of, making it super important for these two to meet up at some point in the final two seasons of Game of Thrones.
The whole idea of keeping Jon's true identity a secret was obviously necessary, since Season 1 saw Robert Baratheon wanting to kill Dany, her unborn child, and Viserys to do away with the Targaryens once more. Had Robert even gotten a whiff of who Jon Snow really is, he would have ordered that the baby be killed before Ned even had a chance to take him back to Winterfell all those years ago. When he tells Ned that he wants them dead, Ned Stark is quick to point out that Robert is going to be killing a child to do away with more Targaryens, but being the Baratheon brute he was, Robert could give no sh*ts about it:
"The whore is pregnant. I warned you this would happen, back in the North. I warned you, but you didn't care to hear. Well, hear it now. I want 'em dead — mother and child both. And that fool Viserys as well."
Now, we can all get behind wanting Viserys dead, because Khal Drogo giving him that famous crown of molten gold was perfect, but this small exchange just shows how deep Robert's hatred for the Targaryens ran, even years later. Now, though, Jon's mother was finally revealed, and his true parentage, which is a lot more important than even his Stark roots. But even if/when he finds out that he's a Targaryen and so closely related to Daenerys, it's anyone's guess what that will come to mean to him.