Game of Thrones: Who Is Jon Snow's Father?

The Season 6 finale of Game of Thrones "The Winds of Winter" gave us a clearer picture than ever of Jon Snow’s mysterious parentage. Let’s dive into those details and see if we can get a better idea of what Jon's family heart tree looks like.
As Bran taps back into the weirwood network of important plot revelations, we return to the pivotal flashback that was abruptly cut off in “Oathbreaker” earlier this season which saw young Ned Stark defeat the Targaryen guards and ascend up the steps of the Tower of Joy. It turns out what awaited him inside was his dying sister Lyanna Stark, who was bleeding out after delivering baby Jon Snow.
So now we finally have confirmation that Lyanna Stark is Jon Snow’s mother. But who is his father?
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In Lyanna’s dying breath, she whispered something in Ned’s ear. “His name is…” she says, with the next part too quiet to hear. It’s safe to assume she named the baby boy Jon, but we don’t know the next thing she told Ned. From the reaction on Bran’s face, who was witnessing the events as a vision-ghost, he did hear what she said, so we’ll probably hear him explain it next season.
Until then, we can interpret the rest of her audible words to glean details that support what book readers have long referred to as R+L=J. Lyanna says, “If Robert finds out, he’ll... You know he will. You have to protect him. Promise me, Ned.” The Robert she refers to is of course Robert Baratheon, Lyanna's betrothed, who started a war to rescue her after, according to Sansa Stark, Rhaegar Targaryen "kidnapped and raped her." But given that she wants Ned to protect the child from Robert, who would surely want to kill the spawn of his great Targaryen enemy, there’s room to interpret that Lyanna was actually in love with Rhaegar and wanted to have his child.

Also, the men guarding the Tower of Joy wore the Targaryen sigil and it was said aloud that they were there on orders from Rhaegar Targaryen. This only strengthens the theory that they were there protecting the love of his life and his child.
And so we are led to the conclusion that Rhaegar Targaryen is Jon Snow’s real father.
What does this mean? Just about every character in the story believes Jon Snow to be the bastard son of Ned Stark, but now it looks like he’s half-Stark and half-Targaryen. He just went from the sullen kid who couldn’t get a seat at the family feast table to a man with a valid claim to the Iron Throne. Rhaegar was the older brother of Daenerys, so that makes Jon the nephew of Dany, which could complicate matters for her when her ships reach Westeros, as his claim to the throne as a male heir would conflict with hers. Not that we think a little thing like a blood relative would stop her and her three battle-ready dragons, mind you.
So after all these hints and visions, the showmakers have given us everything but the final verbal confirmation that Rhaegar and Lyanna are Jon’s parents. There’s still minimal (very, very minimal) room for an extra twist to be thrown in, but this is the going theory on Jon’s parentage based on what we got in this jam-packed episode.

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