Kit Harrington's Jon Snow went on an epic journey in Game of Thrones that took him from being the Bastard of Winterfell to the rightful heir to the Iron Throne. Then, of course, ending the show as a member of the Free Folk. While most of the twists and turns in his arc focused on what it meant for him in particular, one of them righted a very big, almost nonsensical, wrong for another character. That said, this much-needed correction was easy to miss given the narrative density of the HBO adaptation.
Believed to be a Stark by blood for most of Game of Thrones, that turned out to be correct in a different way than what everyone expected. He wasn't the son of Sean Bean's Lord Eddard "Ned" Stark, but rather Ned's sister, Lyanna Stark (Aisling Franciosi). Revealing Ned as Jon's uncle rather than his father was a big moment, but even bigger was the twist that made Harrington's character into royalty in waiting. As Aegon Targaryen, Jon was destined to rule over the Seven Kingdoms. However, the unexpected development is arguably even more important for a key figure in Jon's past.
Making Jon a Targaryen finally redeemed Ned Stark
Something that never sat well with me for most of Game of Thrones was that Ned had apparently been unfaithful to his wife, Catelyn (Michelle Fairley). The show has countless characters that are morally bankrupt, or at least morally grey. Ned was never portrayed as belonging to either of those categories. He was largely one of the show's only truly good men. The presence of Jon as his bastard son was made out to be a stain on Ned's near-flawless soul. Bean's character was loved and respected throughout the Seven Kingdoms, with few having anything legitimately negative to say about him.
So, when it was revealed that Jon's origins were not actually as established, Ned's reputation actually took a posthumous boost. Not only did he not cheat on Catelyn while away from Winterfell, but he raised his nephew as his son, regardless of the risk posed by the possibility of King Robert Baratheon (Mark Addy) finding out. If Robert had discovered a Targaryen remained in Westeros, and that the king's claim to the throne would be challenged, Jon would have been an immediate target. Ned would likely have been honor-bound to turn against his king and best friend to uphold his oath to protect his sister's offspring.
Just to make things even more emotional, Ned even chose to lie to Catelyn to keep Jon safe. The Lord of Winterfell broke his wife's heart and allowed his own reputation to take a huge blow to uphold the deception that Jon was his bastard, and therefore his responsibility to raise. While he could have just lied and told Catelyn that Jon was a foundling, that would have run the risk of Harrington's character being sent away to live elsewhere. There, Jon wouldn't have been under Ned's protection and watchful eye. It was only when Jon joined the Night's Watch that Ned felt confident that his nephew was as safe as he could be away from home, since he still had his uncle Benjen watching over him.
Keeping Jon a Stark was equally important as making him a Targaryen
Even though Jon never actually got to rule as king, he was probably one of the best candidates. His Targaryen lineage gave him the right to do so, but being born of Lyanna Stark and being raised with her house's values was a huge reason why characters like Lord Varys (Conleth Hill) were desperate for Jon to push his claim. If Jon had turned out to be a traditionally pure-blooded, inbred member of the Targaryen family, then his roots in the North and with the Stark family would have been weakened. For narrative reasons, this wouldn't have been nearly as rewarding.
Furthermore, this approach would have made Jon's arc too similar to that of Alfie Allen's Theon Greyjoy. As a ward of Ned Stark, Theon also grew up in Winterfell, understandably feeling like an unwanted outsider. The heir to the Iron Islands ultimately felt torn later in life as he was forced to choose between his actual family and the Starks. Despite basically being a hostage at Winterfell, Theon was largely treated well and became an honorary member of the Stark family. The fact that he wasn't biologically a Stark made his eventual redemption especially powerful.
So, if it turned out that Jon was a full-blooded Targaryen, but still saw the Starks as his family due to being raised by them, then Theon's storyline wouldn't have felt anywhere near as unique. Considering that one of Game of Thrones' biggest strengths is the high quality and wide range of character storylines, Jon's confirmed Stark lineage is just as important as his being unveiled as a Targaryen, too.
Game of Thrones is streaming now on HBO Max.