Game of Thrones spent a lot of its sixth season unraveling mysteries and giving us incredible reveals, including but not limited to Melisandre's true form, Jon Snow coming back from the dead, and Bran finally seeing what happened in the Tower of Joy. While we now know that Ned Stark was not actually Jon Snow's father, as it turns out, George R.R. Martin had been blatantly hinting about the truth for more than a decade. In a fan Q&A from back in 2002, the prominent author was asked who gave Jon Snow, Daenerys Targaryen and Tyrion Lannister their names. The words he chose when answering may surprise you:
Mothers can name a child before birth, or during, or even after; even while they are dying. Dany was most likely named by her mother; Tyrion by his father; Jon by Ned.
The post was unearthed by an enterprising Redditor recently but comes from The Citadel, and shows that while George R.R. Martin blatantly tossed out words like "mother" and "father" when describing Dany and Tyrion's respective parent, he did not do the same for Jon Snow. Instead, when he got to Jon Snow, he instead chose to use the name "Ned" rather than say Jon's parent. George R.R. Martin was super careful, even way back in 2002, to make sure that he didn't formally say Ned Stark was Jon Snow's father. This goes along well with all of the clues he also left in his A Song of Ice and Fire series to make us wonder if the R + L= J theory might be true.
Then, at the end of Season 6, Bran finally made it to another weirwood tree and looked into the time Ned Stark found his sister in the Tower of Joy. He finally fought his way through Rhaegar Targaryen's men and found his sister in the tower. She was happy to see him, but unfortunately she was also dying after childbirth. She whispered something into Ned's ear and Ned took on the responsibility of raising the baby--Jon Snow--and claiming Snow as his own, likely to protect Jon's life. If Robert Baratheon had found out Jon Snow was the son of (presumably) Rhaegar Targaryen all hell would likely have broken loose.
Interestingly, there has been that Game of Thrones Season 6 theory running around the Internet that Lyanna Stark may have whispered a Targaryen name, Jaehaerys, into young Ned Stark's ear just before she passed away. If we were to presume that is true, than Ned Stark actually shortened the Targaryen name to just "Jon" and in that case would only get partial credit for naming Jon Snow. There are plenty of other things that Lyanna could have whispered, including "his house is," so this is going down a rabbit hole in terms of wild Game of Thrones theories, but it is still pretty pleasant to think about.
You can find out what we do know about Game Of Thrones Season 7 with our guide.