Throughout Game of Thrones, there were constantly fan theories about characters and storylines. But one of the biggest mysteries fans would debate was the truth about Jon Snow's parents. Though they were told Jon was the bastard son of Ned Stark, few viewers believed that to be the whole story.

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At the end of season 6, the truth is revealed that Jon is actually the child of Lyanna Stark and Rhaegar Targaryen. And while it came as a shock to many fans, there were plenty of clues along the way that hinted at the reveal that was to come.

Ned Not Telling Jon His Mother's Name

Robert Baratheon in Game of Thrones

In one of the first episodes of the show, Ned and Robert Baratheon discuss their youthful days leading to Robert asking Ned about Jon's mother, to which Ned names her as Wylla. However, in another episode, Jon admits that Ned never told him his mother's name.

It would be unlike Ned to keep that secret from Jon while freely telling Robert. However, it makes more sense if Ned was willing to tell Robert it was some tavern girl just to avoid him from getting more curious about the truth.

Ned And Robert In The Crypts

Ned kneeling in front of Robert in Game of Thrones

After reuniting in Winterfell years after they last saw each other, Ned and Robert take a trip into the crypts of Winterfell to pay respects to Lyanna who is buried there. Even all those years later, Robert still holds onto the pain and anger towards Rhaegar Targaryen.

Robert talks about dreaming of killing Rhaegar every night but Ned is much less vengeful, despite it being his little sister. This hints that he doesn't see Rhaegar as the same monster that Robert does after learning the truth about him and Lyanna.

Jon Has Ned's Blood

Ned and Jon on horseback in Game of Thrones

Game of Thrones can be quite cruel to its fans at times. For instance, the final scene between Ned and Jon as they prepare to go their separate ways on the Kingsroad has Ned promising to tell Jon about his mother the next time they see each other.

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Ned also tells Jon that he might not have his name but he has his blood. It is an interesting way of phrasing it and ends up being true. For those fans who suspected Jon wasn't Ned's real son, it confirms that he is still a Stark.

Stannis's Assessment Of Ned

Stannis Baratheon looking serious in Game Of Thrones

Ned Stark was perhaps the most honorable man on the show and having a bastard son was the one uncharacteristic blemish on his otherwise flawless reputation. However, Stannis Baratheon seems to be the only one who questions that fact.

While at Castle Black and observing Jon Snow as the new Lord Commander, Selyse Baratheon dismisses him as the bastard of some nameless woman. However, Stannis remains skeptical of that as he remarks "That wasn't Ned Stark's way." Despite all his many faults, Stannis may have seen through the obvious lie before anyone else.

Littlefinger Explains The Tourney Of Harrenhal

Littlefinger and Sansa at Lyanna's Grave Game of Thrones

Another hint to the truth is given in the Winterfell crypts in front of the statue of Lyanna. Littlefinger tells Sansa the story of the Tourney of Harrenhal in which Rhaegar Targaryen presented a rose to Lyanna Stark instead of his own wife.

Sansa then reminds Littlefinger of the story's grim ending of Rhaegar kidnapping, assaulting, and killing Lyanna. However, the look Littlefinger gives Sansa suggests that is not the whole story. Given how well-informed Littlefinger is, it is not surprising he knew the truth of their relationship.

Barristan Selmy Remembers Rhaegar

Ser Barristan Selmy inside castle walls on Game of Thrones

As Rhaegar Targaryen died years before the events of the series, viewers only learn about him through the accounts of others. For much of the series, he is presented as the villain who kidnapped Lyanna and kept her locked in a tower which ignited a war.

However, Barristan Selmy was someone who knew him well and called Rhaegar the finest man he ever knew. He also explained that Rhaegar never enjoyed killing and took pleasure in singing. It presents a very different picture of the man and raises the question of if he was really capable of such evil.

The Death Of The Targaryen Children

Ned takes Jon Snow after Lyanna's death in Game of Thrones

When it comes to Robert's Rebellion, it is not the heroic victory many people make it out to be. Among the atrocities committed, Tywin Lannister had all the remaining Targaryen children butchered which Robert forgave him for.

It is later revealed that Robert is willing to have Daenerys and her unborn child assassinated, much to Ned's disapproval. The cruelty Robert is capable of alludes to Ned's wise decision to hide Jon's true identity from his friend and why he would see that as necessary.

Daenerys's Vision

Daenerys in front of the Iron Throne in Game of Thrones

In season 2 of the show, Daenerys is presented a vision by the magical warlocks of Qarth. Along with seeing her beloved Khal Drogo, Daenerys also has a vision of the Iron Throne as snow falls on it.

This vision could be interpreted in many different ways. It could be showing her the future in which she wins the Iron Throne as winter descends. It could be a hint that Jon Snow would eventually sit on the Iron Throne. But it seems to be an early clue that Jon is actually the rightful heir to the throne instead of Daenerys.

A Targaryen Alone In The World

Aemon looking intense in Game of Thrones

Another character who is hiding a big secret about their family is Maester Aemon who reveals to Jon in season 1 that he is actually Aemon Targaryen. The connection between these two characters is never revealed to either of them before Aemon's death, but there is a clever allusion made.

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In one episode, Sam tells Aemon the news they have heard about Daenerys Targaryen across the Narrow Sea. Aemon laments that he is too old to reach out to this young relative of his, saying "A Targaryen alone in the world is a terrible thing" and at that exact moment, Jon Snow enters the room.

Ned's Confession

Ned Stark lifting his head at his execution in Game of Thrones

Though Ned's honor is his biggest trait, it is tested quite often in the corrupt world of King's Landing. In one episode, Maester Aemon asks Jon if Ned would choose honor or family if faced with that decision and Jon is sure Ned would always do whatever was right.

However, when charged with treason, Ned confesses to the false crime in order to save Sansa. The fact he willingly sacrificed being deemed a dishonorable man in order to help his loved ones foreshadows the reveal that he was willing to stain his honor years earlier by pretending Jon was his child.

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