In AGoT, chapter 35, Eddard IX, Littlefinger takes Ned to Chataya’s brothel to see Robert’s youngest bastard child. After the interview, as they ride away, Ned’s thoughts become introspective:

“For the first time in years, he found himself remembering Rhaegar Targaryen. He wondered if Rhaegar had frequented brothels; somehow he thought not.”

This is a puzzling thought, since a closer look reveals that not only has Ned thought of Rhaegar recently, he thinks of him frequently. There are six previous sustained thoughts or conversations about Rhaegar in prior Eddard POV chapters. That means in seven out of nine of his POV chapters to that point, Ned thinks about or mentions Rhaegar. So what’s going on here?

It has been noted that Ned never seems to have a negative thought about Rhaegar. This is used to support the idea that Ned knows that Rhaegar was not the kidnaping rapist Robert thinks he was. This particular thought actually goes a long way in that department– Ned compares Robert to Rhaegar and Robert comes up wanting. Since we know that Ned himself is not the type to frequent brothels (to Petyr Baelish’s evident glee– he delights in making Ned uncomfortable by taking him to these places, as we see on two separate occasions) we can assume that with this particular comparison he is thinking of Rhaegar as a man of honor like himself.

To review Ned’s previous thoughts and conversations about Rhaegar is revealing and gives a clear picture of how Ned perceives Rhaegar. Beginning in AGoT, chapter 4, Eddard I, when Ned and Robert are in the Winterfell crypts visting Lyanna’s tomb, Robert is overcome with emotion and tells Ned:

“I vowed to kill Rhaegar for what he did to her.”

 The exchange continues:

“You did,” Ned reminded him.

“Only once,” Robert said bitterly.

They had come together at the ford of the Trident while the battle crashed around them, Robert with his warhammer and his great antlered helm, the Targaryen prince armored all in black. On his breastplate was the three-headed dragon of his House, wrought all in rubies that flashed like fire in the sunlight. The waters of the Trident ran red around the hooves of their destriers as they circled and clashed, again and again, until at last a crushing blow from Robert’s hammer stove in the dragon and the chest beneath it. When Ned had finally come on the scene, Rhaegar lay dead in the stream, while men of both armies scrabbled in the swirling waters for rubies knocked free from his armor.

“In my dreams, I kill him every night,” Robert admitted. “A thousand deaths will still be less than he deserves. “

There was nothing Ned could say to that.

Ned thinks about this scene, the death of the man who allegedly kidnaped and raped his sister (“How many times… How many hundreds of times?”), extremely dispassionately. Robert is still full of hate, but Ned manages only polite pauses and quiet sympathy. First hint that all is not as it seems! The scene proceeds into a discussion of Jon Arryn’s son being fostered by the Lannisters:

Ned would sooner entrust a child to a pit viper than to Lord Tywin, but he left his doubts unspoken. Some old wounds never truly heal, and bleed again at the slightest word. […] “Lysa ought to have been honored. The Lannisters are a great and noble House.” […] “I have more concern for my nephew’s welfare than I do for Lannister pride,” Ned declared.

Here we have an example of Robert avoiding all those unpleasantries he doesn’t care to deal with, hiding behind the “nobility” of his in-laws. Ned isn’t fooled as he recognizes the true nature of House Lannister and their regard for the lives of children, and has a much more vehement reaction to the fostering of his wife’s nephew than he does to the supposed kidnap and rape of his own sister.

In chapter 12, Eddard II, Robert raises the issue of Daenerys Targaryen and her unborn child. Ned strongly objects to the murder of children.

“He remembered the angry words exchanged when Tywin Lannister had presented Robert with the corpses of Rhaegar’s wife and children as a token of fealty… It was said Rhaegar’s little girl had cried as they dragged her from beneath her bed to face the swords.”

For Ned, the murder of children was and is unspeakable. But Robert has not gotten over his hatred of Targaryens

“Unspeakable? The king roared […] “And Rhaegar… how many times do you think he raped your sister? How many hundreds of times?”

It is clear from Ned’s POV that the Lannister crimes far outweigh those of Rhaegar Targaryen, as the conversation continues to a discussion of Jaime as the Warden of the East. Ned is disturbed at placing so much power in the hands of one family. He recalls the aftermath of the Trident, the Sack of King’s Landing and the death of Aerys Targaryen.

“You took a wound from Rhaegar,” Ned reminded him […] “The remnants of Rhaegar’s army fled back to King’s Landing. We followed… I expected to find the gates closed to us [but] the lion of Lannister flew from the ramparts, not the crowned stag. And they had taken the city by treachery.”

At the center of the most dishonorable actions of the war in Ned’s memory is not Rhaegar Targaryen, but the Lannister family. Robert disagrees:

“Treachery was a coin the Targaryens knew well,” Robert said. The anger was building in him again. “Lannister paid them back in kind. It was no less than they deserved. I shall not trouble my sleep over it.”

“You were not there,” Ned said, bitterness in his voice. Troubled sleep was no stranger to him. He had lived his lies for fourteen years, yet they still haunted him at night. “There was no honor in that conquest.”

“The Others take your honor!” Robert swore. “What did any Targaryen ever know of honor? Go down into your crypt and ask Lyanna about the dragon’s honor!”

“You avenged Lyanna at the Trident,” Ned said, halting beside the king. Promise me, Ned, she had whispered.

Here we have a stark (forgive the pun 😉 ) contrast between one view of honor and another. In Ned’s view, the killing of children is the height of dishonor. He harks back to his promise to his sister here, which is most likely inspired by his recollection of what the Lannisters did to Rhaegar’s children in King’s Landing. When Robert urges him to “ask Lyanna” Ned recalls the promise she extracted from him. Robert has different views of honor, informed at least in part by his interpretation of R+L. Their earlier exchange in the crypts supports the notion that Ned does not in any way share that interpretation. Robert’s notion that Lysa should have been “honored” by his plan to hand her son over to the Lannisters proves his utter obliviousness to the brutal nature of Lannister policy.

Chapter 16, Eddard III finds the royal party at the Darry holdings. Arya has been accused of attacking Prince Joffrey, and after days on the run has been found and brought before the Queen in the Darry audience chamber. Ned recalls:

“Ser Raymun lived under the king’s peace, but his family had fought beneath Rhaegar’s dragon banners at the Trident, and his three older brothers had died there, a truth neither Robert nor Ser Raymun had forgotten.”

Once again we have a memory of Rhaegar Targaryen and of the war fought against his House, contrasted with the actions of the Lannister family. While Ned hardly expects the Targ loyalist Darrys to support him in the matter of Arya and her wolf, in his mind, as always, the clear and present danger comes from House Lannister.

Chapter 20, Eddard IV the party has finally reached King’s Landing. After an emergency meeting of the Small Council, Ned is taken by Littlefinger to see Catelyn at her hiding place in a brothel in the city. She tells him of the attempt on Bran’s life, shows him the scars on her hands and the dagger that made them, and accuses Tyrion Lannister of hiring and arming the assassin. Ned refuses to believe that Tyrion could have acted alone and Littlefinger insinuates he did not. Ned cannot accept that Robert might have knowledge of this act…

“Yet even as he said the words, he remembered that chill morning on the barrowlands, and Robert’s talk of sending hired knives after the Targaryen princess. He remembered Rhaegar’s infant son, the red ruin of his skull, and the way the king had turned away, as he had turned away in Darry’s audience hall not long ago. He could still hear Sansa pleading, as Lyanna had pleaded once”

Here we are again, with a memory of Rhaegar paired with Lannister infamy, in both past and present. In this passage there is a clear connection between Robert’s acceptance of child slaying, Ned’s anxiety over it, the protection of innocents, and a young woman pleading for mercy. If Sansa was pleading for Lady’s life, what could Lyanna have been pleading for if not her son? Who posed the danger to Rhaegar’s children, to Lady, and allegedly to Ned’s own son Bran? None other than House Lannister. Hidden beneath the overt memories and never mentioned explicitly, yet undoubtedly heightening Ned’s anxiety given the nature of his train of thought, is the fact that the child that he promised to protect from Robert’s fury and the Lannister willingness to enable him as a killer of innocents has been sent into the far North in the company of the very Lannister now accused of trying to harm Bran.

Chapter 30, Eddard VII is even more explicit in the connection. Ned finally connects with the Robert he once knew, and seems on the verge of finding proof of Lannister perfidy once and for all. Knowing that if he finds this proof, it could mean war, he thinks

“…if Lord Tywin dared to rouse the west, Robert would smash him as he had smashed Rhaegar Targaryen on the Trident.”

The Lannisters, architects of cruelty and dishonor in Ned’s POV, seem poised to meet their end in the face of Robert’s fury and Ned is both cautiously optimistic and relieved at the prospect.

Chapter 33, Eddard VIII finds things have taken a turn away from the “old” Robert at a Small Council meeting. Robert is resolved to send hired killers after the pregnant Daenerys Targaryen. Ned is furious and refuses to sign off on the plan. Their bitter quarrel of fifteen years previous seems to come to life all over again:

“Your grace, I never knew you to fear Rhaegar.” Ned fought to keep the scorn out of his voice, and failed. “Have the years so unmanned you that you tremble at the shadow of an unborn child?”

This is the second time Ned mentions Rhaegar aloud. Both mentions are to Robert during moments of truth telling. The latter time is highly provocative, but in both cases the initial subject matter is Daenerys Targaryen and the killing of children. In fact, more often than not, when Ned thinks about Rhaegar Targaryen it is connected to his death, his slain children, the threat to his young sister, and the role House Lannister has played in turning Robert into a child killer.

I believe this is highly revealing of Ned’s motivating anxiety, and when he meets Barra he realises in the course of his discussion with Littlefinger the danger she is in from the Lannisters.

 “…Robert got a pair of twins on a serving wench at Casterly Rock […] Cersei had the babes killed and sold the mother to a passing slaver.”

Ned reflects that the Robert he once knew would never have condoned such a thing, but now he’s not so sure, as Robert has become “practiced at shutting his eyes to things he did not wish to see.”

Back to the exchange with Barra’a mother which would lead once more to thoughts of Rhaegar, it began:

“I named her Barra,” she said as the baby nursed. “She looks so like him, does she not, milord? She has his nose, and his hair…”

“She does,” Eddard Stark had touched the baby’s fine, dark hair. It flowed through his fingers like black silk. Robert’s firstborn had had the same fine hair, he seemed to recall.

“Tell him when you see him, milord, as it… as it please you. Tell him how beautiful she is.”

“I will,” Ned had promised her. That was his curse. Robert would swear undying love and forget them before evenfall, but Ned Stark kept his vows. He thought of the promises he’d made Lyanna as she lay dying, and the price he’d paid to keep them. […]

Here we have Ned making a promise to a young mother regarding her child and suspiciously, it reminds him of the promises he made to his dying sister. All the way back in Eddard I, he recalled that moment:

 “Promise me, she had cried in a room that smelled of blood and roses. Promise me, Ned. The fever had taken her strength and her voice had been faint as a whisper, but when he gave her his word, the fear had gone out of his sister’s eyes. Ned remembered the way she had smiled then, how tightly her fingers had clutched his as she gave up her hold on life…”

Not only does the promise remind Ned of his sister, but the young girl’s reaction is highly evocative of Lyanna’s:

She smiled then, a smile so tremulous and sweet that it cut the heart right out of him. Riding through the rainy night, Ned saw Jon Snow’s face in front of him, so like a younger version of his own. If the gods frowned so on bastards, he thought dully, why did they fill men with such lusts?

In this situation, Ned’s train of thought has gone from young girl with infant to promises to his dying sister and now to Jon Snow. Surely there is a clear connection, even a mirroring, of the two situations? His anxiety over the fate of Barra leads him to this bizarre thought about Jon Snow. Often used as proof that Ned thinks of Jon as his bastard or, alternatively, to question the conclusion that R+L=J was a legitimate union, I believe this thought is more complex. As Ned rides off, concerned for the infant and mother he has just met, he thinks of Jon Snow. Since he has just been thinking of his sister, this seems natural enough. It is the fact that he has been thinking about the promises made to his sister that I believe leads to the thought about bastards. In order to fulfill his promises to Lyanna, Ned has had to raise Jon as his own bastard, denying him something that is his by right and making him equal in status to the bastard daughter of a whore in King’s Landing. This is part of the price he has paid to keep his promise, and the reason he thinks of Jon in the context of bastards being frowned on by the gods. Like his concern for the safety of the children, this is all part of his hidden anxiety. Furthermore, we should note the phrase “Ned Stark kept his vows.” This POV assertion by Ned that he is a man who keeps his vows stands in direct contrast to the notion that this passage affirms that Jon is Ned’s bastard. Since he has earlier admitted to Robert that Jon Snow was born after his marriage to Catelyn, I believe this is a subtle hint that Ned has not forsworn himself in any way and that by raising Jon as his own son he has in fact been engaged solely in fulfilling a vow made to his dying sister. Finally, here is where the train of thought becomes quite curious. After a verbal exchange with Littlefinger about Robert’s bastards, wherein he learns about Cersei’s willingness to dispose of them, he comes to thought we opened with

“For the first time in years, he found himself remembering Rhaegar Targaryen. He wondered if Rhaegar had frequented brothels; somehow he thought not.”

Since we have clearly established that Ned thinks of Rhaegar often, there must be some hidden explanation for this thought. As it has been demonstrated that Ned’s thoughts about Rhaegar generally center around his death, child slaying and the perfidy of House Lannister, I think the difference is that here he (“for the first time in years”) allows his thoughts to go one step further and thinks about Rhaegar as Jon’s father. His unspoken thoughts have now gone from his sister, to promises, to Jon Snow, to bastards in brothels, to Rhaegar Targaryen and, interestingly, we arrive at the conclusion that Rhaegar would not have frequented brothels. Meaning? Ned unconsciously allows himself to think about Rhaegar as the father of his sister’s child, compares him to Robert who father’s bastards in brothels and with serving wenches, and upon reflection decides that Rhaegar would not behave in this way. Surely if Ned believed that Rhaegar had fathered a bastard child on his beloved sister, he would not reach such a charitable conclusion? I believe that here, in this passing thought, we have proof from Ned’s own thoughts, as compelling as the scene from the Tower of Joy, that Ned is aware of Jon’s legitimacy. Furthermore, taken as a whole, Ned’s collective thoughts about Rhaegar support the notion that he bears no ill will for the dead prince. Interestingly, close examination has also shown that Ned has seen with clear eyes that the true enemy of the Crown in his lifetime has been House Lannister.