Spoilers for all published books in A Song of Ice and Fire.
This is one of those “Yeah, it’s basically canon” ones. The most famous of all Game of Thrones fan theories, R+L=J posits that Jon Snow is not the child of Ned Stark, but of Ned’s sister Lyanna and Rhaegar Targaryen, meaning Jon would be Daenerys’ nephew and the first (possible) secret Targaryen to show up on this list.
There’s actually a startling level of evidence in support of this theory. One: We know Lyanna made Ned promise her something before she died. We’re meant to assume it was to take her body to Winterfell, but that’s never explicitly stated. And for the amount of time Ned spends dwelling on it, that would be a pretty innocuous promise. Ned promising to raise Jon and protect him from King Robert Baratheon’s anti-Targaryen rampage is much more weighty. The only Stark children who don’t look like Catelyn are Jon and Arya… who, we’re told, looks like Lyanna. Ned doesn’t seem to hate Rhaegar, which is weird if Rhaegar raped his sister. At one point Ned’s ruminating over about King Robert’s bastards, which you do, and from there he starts thinking about his (presumed) bastard Jon, which you do… and then his train of thought takes him to Lyanna and Rhaegar for some reason. Bzuh? And, most telling: In her vision at the House of the Undying Daenerys sees a blue winter rose growing out of a chink in a wall of ice. The blue winter rose is clearly established elsewhere in the series as a symbol for Lyanna, specifically for her death. And who’s set up shop at a Wall of ice…?
We know—or, at least, we think we know—that there are going to be three Targaryens kicking butt and taking names on Daenerys’ dragons by the end of the series. The only even slightly compelling reason, for me, that Jon would not be one of those Targaryens is that it’s just too obvious at this point that he would be. But if Daenerys is one of the Targaryens, and Jon is the second, who’s the third…?
Tyrion Lannister Is a Secret Targaryen
This theory posits that Tyrion is the son of King Aerys (Daenerys’ father), who raped Tywin’s wife Joanna. There’s not a heck of a lot of evidence for it—we know Joanna spent some time at King’s Landing. We know Aerys *cough* liked her. We know he’s the sort of guy who would not hesitate to rape someone, even the wife of one of his allies. We know Tyrion has one purple eye and blonde hair so light it’s almost white, purple eyes and white hair being Targaryen coloring. And we know Tywin hates Tyrion, which could be because Tyrion’s not his son… or it could be because Tywin’s just a jerk like that. I could be wrong, but to me this theory reads solely as wishful thinking. Who wouldn’t want to see Tyrion Lannister on the back of a dragon raining hellfire down on those who wronged him? But it probably won’t happen.
…and Screw It, So Is Meera Reed
You get a secret Targaryen backstory! And you get a secret Targaryen backstory! Everyone gets a secret Targaryen backstory! This theory has Meera Reed as the Leia to Jon Snow’s Luke—the twin sister he was separated from at birth. She and Jon are the same age, and they look (vaguely) alike. Meera’s temperament is similar to what we know of Lyanna—free-spirited and not averse to doling out butt-whuppings. Greywater Watch, the seat of House Reed, would be the perfect place to hide a secret Targaryen, because it’s pretty much impenetrable. And the mysterious Howland Reed, as Ned Stark’s closest friend and ally, would be just the person he would give the second child to. The people who buy this theory are drawn in less by the sort of evidence that R+L=J has (it’s just not here in this case) and more by the neat—and certainly unexpected—way in which it gives us the third head of the Targaryen dragon.
Speaking of the Reeds—Howland Reed is the High Sparrow
One of the major sea changes in A Dance With Dragons is that religion starts messing stuff up in a big way for our King’s Landing characters. At the fore is the High Septon, aka the High Sparrow, who swoops out of nowhere as the leader of a new religious movement, becomes basically the Pope of Westeros, and tricks Cersei into letting him have his own private army. He’s incredibly significant, but we know next to nothing about him. The yin to that yang is Howland Reed, father to Jojen and Meera, one of Ned Stark’s closest allies, one of the few characters in a position to know whether R+L=J is true or not, and… completely absent from the story so far.
The physical description of the High Sparrow is similar to how people from Reed’s neck of the woods are described. The Sparrow has no lost love for Cersei and a soft spot for Ned Stark. And there are hints that Martin’s setting up a Revenge of the North plotline. Arya’s learning the ways of murder in Braavos. Wyman Manderly’s on the verge of bringing Rickon back. Sansa’s getting closer and closer to coming into her own politically. All this as the Lannisters lose their grip on power. A reveal that Ned Stark’s best friend has essentially infiltrated King’s Landing under the guise of religion would be fitting and so, so sweet.