WARNING: SPOILERS FOR THE SEASON SIX FINALE OF GAME OF THRONES INSIDE:
[UPDATE – 6/26/16 11:48PM EDT] – IGNORE ME!!! This is a lesson on why you always watch shows with the closed captions on. Lyanna did know Robert would have Jon killed. (or did she mean he'd have Rhaegar killed, not knowing he was already dead?) The show also just used [whispering] in Lyanna told Ned what she had named her infant son. Guessing it wasn't “Jon.”
ORIGINAL ARTICLE BELOW:
After years – or in the case of some book readers, decades – of waiting, Game of Thrones finally confirmed Ned Stark is not Jon Snow”s father. While Lyanna Stark didn”t turn to the camera and explicitly state “Ned, this baby came from my womb and was put there by Rhaegar Targaryen. Name him Jon,” as her dying words, the writing is on the wall. R+L does indeed equal J.
Sure, the show didn”t go into detail as to whether Jon was the product of rape or a love affair. Sure, it didn”t explain how Ashara Dayne and her bastard child with Brandon Stark got mixed up in the backstory of Jon”s infancy. But Game of Thrones did confirm one thing. Why Lyanna made Ned promise to keep Jon safe. The reason was both tragic and unexpected, at least for me.
For years, the prevailing theory was Lyanna wanted Ned to keep her baby safe from Robert Baratheon. When Rhaegar fell to Robert”s sword on the Battle of the Trident, the Targaryen reign came to an abrupt end. King Robert and Tywin Lannister ordered the execution of every living Targaryen, including Rhaegar”s infant children and any bastards fathered by Targaryen nobility. Knowing her fiancé would have her baby boy murdered for his bloodline, fans reasoned, Lyanna convinced Ned to choose familial loyalty over his friendship with Robert. But that was not the case.
In case you don”t recall, a brief history of how everyone ended up at the Tower of Joy: During the Tourney at Harrenhal, Rhaegar crowned Lyanna Stark the Queen of Love and Beauty instead of his wife, Elia Martell. This was a bit of a scandal. Approximately a year later, Lyanna was riding through Riverlands when she was abducted by Rhaegar and several of his men, including Arthur Dayne. Whether she rode out to meet them or not is unknown. Together, Rhaegar and Lyanna traveled to Dorne, where they holed up in the Tower of Joy and Lyanna fell pregnant with Jon.
Meanwhile, for the love of his sister”s besmirched honor, Brandon Stark went to King”s Landing to demand her release and the death of Rhaegar. You do not demand things of the Mad King, especially that he kill his son. Rickard Stark was called to the Red Keep to collect his son. Things went quickly south, as Aerys decided to burn Rickard alive. There was a caveat. If Brandon Stark could reach his father and cut him free, they could leave. However, Brandon was attached to a cord that strangled him as he tried to reach the longsword, and both men died. Or, in the words of Jaime Lannister:
“Five hundred men just stood there and watched. All the great knights of the Seven Kingdoms. You think anyone said a word, lifted a finger? No, Lord Stark. Five hundred men and this room was silent as a crypt. Except for the screams, of course, and the Mad King laughing. And later… when I watched the Mad King die, I remembered him laughing as your father burned… it felt like justice.”
It was this cruelty that flung the kingdom into full-blown civil war as the Starks, Baratheons, Arryns Tullys, and all their banner men declared open Rebellion. The war would end when Robert killed Rhaegar and Jaime killed King Aerys. It was in the aftershocks of the war, when Robert was in the process of being crowned, that Ned ran south to save Lyanna from the Tower of Joy.
This is where Bran”s visions come in. During the Tower of Joy flashback in “The Winds of Winter,” Lyanna whispers her final words to Ned. We can”t make out everything, but this much is clear: Lyanna feared HER FATHER would have Jon killed. Not Robert. All of this – from abduction to dynastic downfall – happened within the span of a year (assuming Lyanna didn”t get pregnant right away and/or was not already pregnant at the time of her “kidnapping”.) Rhaegar had kept the events triggered by their abduction and/or romantic tryst well-hidden from his baby-mama. What version of the facts he fed her before he went to his death at the head of the Targaryen army is unknown. But Lyanna died never knowing her father was dead, much less the sadistic manner of it.
So here Ned Stark is, promising his dying sister that he will keep her bastard boy safe from a man who died trying to protect her honor. She had no idea Robert would order all the Targaryen children murdered. Ned made that choice on this own. To honor his dying sister's wish, even at the cost of his own marriage. That”s the most Ned Stark thing to ever happen.