Fans knew. Bran knew. Sam knew. Even Rhaegal the Dragon knew. And now, Jon Snow finally knows too: He is the son of Rheagar Targaryen and Lyanna Stark — which means he’s a trueborn Targaryen, and not a bastard.
Samwell Tarly disclosed this information to the King of the North during the first episode of the eighth and final season of Game of Thrones. Bran and Sam had put together the clues last season: Sam and Gilly found documents at the Citadel that showed Rhaegar had annulled his marriage to Elia Martell and eloped with Lyanna Stark afterward.
Bran used his greenseer abilities to travel through time and observe the secret marriage of the two lovers and Jon’s birth in the Tower of Joy. This means that Jon is not the bastard son of Ned Stark, as everyone long assumed. The fact that Rhaegar and Lyanna were legally married means that Jon is not a bastard, but rather the direct inheritor to the Iron Throne.
Jon and Daenerys might have even had an clue of Jon’s true inheritance too: Earlier in the episode, Jon rode Rhaegal, Daenerys’ dragon who is named for his own father Rheagar, in spite of the fact that only Targaryens have been able to ride dragons in the past.
“Your mother was Lyanna stark. And your father, your real father, was Rhaegar Targaryen. You’ve never been a bastard. You’re Aegon Targaryen, true heir to the Iron Throne,” Sam tells Jon in the crypts. “I’m sorry. I know it’s a lot to take in.”
Jon reacted to the exposure with indignation, disappoint that his father figure Ned Stark had lied to him for so long. “My father was the most honorable man I’ve ever met,” Jon retorts. “You’re saying he lied to me all my life?”
“Your father, well, Ned Stark. He promised your mother he’d always protect you. And he did. Robert would have murdered you if he knew. You’re the true king. Aegon Targaryen, Sixth of his Name, Protector of the Realm, all of it.”
The last time Ned and Jon spoke in season 1, Ned promised to tell Jon who is mother was when they met again. But Ned was killed on the orders of Joffrey Baratheon and never saw Jon again.
Sam, the sensitive counterpoint to a very blunt Bran, clarified to Jon that Lyanna swore Ned to secrecy. Had Robert Baratheon known the identity of Jon’s real father, he would have tried to kill him, just as he tried to kill Daenerys.
Which brings us to the elephant in the room: Jon and Dany consummated their growing romantic relationship in the season 7 finale. After Bran and Sam’s expose, Jon finally knows that he and Daenerys are aunt and nephew. On a personal level, Jon will perhaps have hang-ups about what happened between them:
After all, the Starks recently fought a war to dethrone a king made mad by generations of incest. Daenerys, who comes from a long line of Targaryens who married their siblings and cousins, might be more open to continuing their relationship and union.
Daenerys will possibly be more worried with Jon’s newfound claim to the Iron Throne. Traditionally, male heirs have been given preference over female ones in Westeros — though Queen Cersei does presently sit on the throne. What’s more, Jon is the son of the Mad King Aerys’ eldest child and therefore, some would disagree, a more direct successor than Dany.
Fortunately for Daenerys, Jon Snow has never uttered a desire to rule anything or anybody. He’s only taken on leadership roles when they are foisted upon him, or help resolve a larger problem. Presently, he’s more worried with the approaching war with the Night King and the White Walkers.
So there’s a fine opportunity he’ll offer to surrender his power to her. It remains to be seen how the rest of Westeros might feel about that.