Bran Stark and Sam Tarly pieced together the puzzle of Jon Snow's parentage, his legitimacy and his claim to the Iron Throne tonight, in a flashback that confirmed Jon is not a bastard and this his real name is Aegon Targaryen.
Sam (via Gilly in an earlier episode) was able to complete the picture for Bran, who was aware that Jon was the son of Rhaegar Targaryen and Lyanna Stark from his Tower of Joy flashback, but not that High Septon Maynard had annulled Rhaeger's marriage to Elia Martell before remarrying the prince to Lyanna.
Bran noted how this all meant that Robert's Rebellion, the civil war that set up the events of Game of Thrones, was based on a lie.
This is because - and you can be forgiven for not remembering as we never witnessed it on screen - a major catalyst in the war between House Baratheon (supported by houses Stark, Arryn, Tully, Lannister and Greyjoy) and House Targaryen (supported by houses Tyrell and Martell) was the supposed 'abduction of Lyanna Stark'.
It was widely believed that Prince Rhaegar, heir to the Iron Throne, kidnapped Lyanna, Ned's sister who was betrothed to Robert Baratheon.
The event was even more controversial as Rhaegar was thought to still be married to Elia Martell.
The Game of Thrones Wiki explains what went down after the "kidnapping":
The abduction kickstarted the war, then, though Lyanna in fact chose to run away with Rhaegar.
The episode also disclosed Jon Snow's real name - Aegon Targaryen. Aegon was also the name of Jon's older brother, who was brutally murdered by Ser Gregor 'The Mountain' Clegane during the Sack of King's Landing. If Jon sits on the Iron Throne before the show finishes, he will be King Aegon IV Targaryen.
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