Warning: Season six spoilers below.The season six finale of "Game of Thrones" finally confirmed Jon Snow's lineage, well, basically.Bran Stark, now the Three-Eyed Raven, finally went back to complete the Tower of Joy vision and confirmed what many fans have been predicting for decades: Jon Snow is the son of Lyanna Stark, Ned Stark's sister.As Ned finds his younger sister dying from the complications of childbirth in the tower, she whispers into his ear and tells him to protect her young child. Even though we now know for sure that Jon is Lyanna's son, we don't know if his real name is Jon thanks to a muted whisper from Lyanna or who his father is, but the theory holds that Jon's father is Rhaegar Targaryen.So who exactly is Rhaegar Targaryen'Rhaegar was the eldest son of the Mad King Aerys II Targaryen, which also makeshim Viserys and Daenerys' older brother.As Westeros history holds, Ned Stark and Robert Baratheon were best friends. Robert was betrothed to Lyanna, while Rhaegar, heir to the Iron Throne, was married to Elia Martell, Oberyn's sister.But soon, Rhaegar and Lyanna disappear, and Rhaegar was accused of her abduction. This led to Robert's Rebellion, which ultimately resulted in Rhaegar's death and the fall of House Targaryen.Rhaegar diedbefore Dany was even born when Robert defeated him at the Battle of the Trident. After Tywin Lannister's forces conquered King's Landing and Jamie Lannister killed the Mad King, Viserys and an infant Dany escaped from Westeros. Rhaegar's wife, Elia, and their two children were murdered. Even though Ned found his sister, he was unable to save her from childbirth complications, but history marks her as a casualty of war.After the war, Ned returned with a child and told everyone it was his bastard son. But Sunday night's episode showed that the baby was in fact his nephew. Ned kept this secret from his best friend Robert and from his own wife, Catelyn, presumably to keep the child safe. If Robert, or anyone else for that matter, knew that the child was a Targaryen, he would be in danger.If Rhaegar had kidnapped Lyanna against her will, she didn't make that known in her final moments. She loved the child she handed over to her brother and made him promise to take care of him. Rhaegar also had a reputation of being a kind and noble man, which would make a senseless kidnapping out of character.Ser Barristan Selmy, one of the most noble knights from Westeros, told Dany that her brother was the "finest man I ever met" back in season three. And in season four, Oberyn simply says Rhaegar left his sister for another woman, which would be Lyanna.Littlefinger also shares a story in season five that explains how Rhaegar rode past his own wife after winning a tourney to lay roses in Lyanna's lap. After all of these clues, it's to be expected that Lyanna and Rhaegar had a relationship that just couldn't survive.If Rhaegar is Jon's father, that makes Dany his aunt, and also makes him a part of two very powerful houses. He is fire and ice.Join the conversation about this storyNOW WATCH: An exercise scientist reveals exactly how long you need to work out to get in great shape
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