"Game of Thrones" Season 6 episode 3 took fans to the time when Lord Howland and Ned Stark visited the Tower of Joy and killed Ser Arthur Dayne. This particular scene gives way to quite a few fan theories, including Jon Snow's (Kit Harrington) parentage and a newer theory about Bran Stark's (Isaac Hempstead Wright) role in the series.
The Tower of Joy scene preludes the events in the George RR Martin books, where Ned finds his sister Lyanna in a pool of blood, which is theorised to be due to childbirth. Ned makes a promise to her before she passes away, but it is not revealed to the reader.
The theory "R+L=J" is born out of this storyline. It suggests that Lyanna gave birth to a baby boy fathered by Rhaegar Targaryen, who she willingly ran away with. This would make the baby a Targaryen-born, making Ned's nephew a threat to Robert Baratheon.
In order to protect the baby from the wrath of Robert and away from the manipulations of the Lannisters, Ned raises the child as his b------ son, Jon Snow.
Now along with this theory, the Tower of Joy scene from Season 6 episode 3, "Oathbreaker," has also given rise a newer one that holds Jon's younger half-brother Bran responsible for everything gory in "Game of Thrones."
The theory, shared by NegativeKarmaSnifer on a "Game of Thrones" Reddit page, reads:
From S6E3, Bran realizes that others can hear him during the visions from the past, but doesn't understand that they cannot fully understand him.
He attempts to reason with King Aerys when shown a vision of him.
The King only hears whispers, and is driven mad by it.
Bran tries to fix this, however makes it worse.
Mad King Aerys burns Bran's grandfather alive while Bran frantically tries to stop him.
All he hears is whispers.
Bran sets the events of the show in motion.
Fans will remember how Bran discovered the incestuous relationship between Jamie (Nikolaj Coster-Waldau) and Cersei (Lena Headey) in Season 1 episode 1 of the show. Jamie had pushed him out of the high window of the tower he was peeping in from, which is what set off the events in the show. The new fan theory suggests that Bran has always been and will always be central to the events of "Game of Thrones."