At Winterfell, Jon has introduced Daenerys to his family and the North as his Queen. It's clear to everyone who knows him well that Jon is in love with her. Sam is left with the task of telling him the truth about his parentage.
It was late in the evening before Jon and Daenerys had been finally left alone in the great hall of Winterfell. They had thought they might have a moment together before they had been interrupted yet again, this time by Sam. Jon had let him stammer on for a while about Oldtown and The Citadel, but it was getting late and there was nothing to be said that couldn't wait till morning.
"You can leave now Sam," Jon said kindly but pointedly, watching Sam as he hovered awkwardly in the middle of the room, unsure of what to do with himself.
Daenerys sat by the hearth with Ghost sleeping at her feet. Jon caught the hint of a smile on her face as their eyes met briefly. It had been a long day and all he wanted was to fall into bed with this woman and forget their troubles for a while.
"Actually," Sam said, clearing his throat uncomfortably, "I need to speak with you Jon…"
"You've been speaking Sam," Jon muttered.
"... I need to speak with you alone," Sam said, before turning quickly to Daenerys and giving a small bow, "Begging your pardon, Your Grace."
Daenerys raised her eyebrows in surprise, it was a rare occasion that she was asked to leave.
Jon sighed. He had been arguing with his sisters and the Northern lords all day about his newfound allegiance to the Dragon Queen, he didn't need this from Sam too. "I have pledged myself and the North to Daenerys. She is our Queen now. Anything you have to say to me can be said in front of her."
"I understand that," Sam said, "But this is rather… personal."
"Is it Gilly?" Jon asked quickly, "Did something happen?"
"Not Gilly… No…" Sam stammered.
"Well spit it out then," Jon said, rubbing his eyes and looking exhausted.
Sam's eyes shifted from Jon to Daenerys and back again. Daenerys sat calmly next to the crackling fire, watching the scene play out.
"Its about…- Its about your mother," Sam stuttered.
"My mother?" Jon looked up with a start, surprise written across his face.
Sam nodded.
"Do you…- What about her?" Jon asked in confusion.
There was a long pause as Sam hesitated, seeming not quite sure how to get out the words now the time had come to tell them.
The silence was broken by Daenerys soft voice. "Perhaps I shall retire after all," she said standing to leave, sensing that despite Jon's assurances, this was a conversation best had in private.
"No, wait," Jon said, reaching for her as she moved to leave the fireside. He caught her by the arm and they met eyes, the familiar spark between them flared.
"Stay." Jon said quietly. Daenerys watched him for a moment longer then nodded and took her seat again.
Sam watched all of this uncomfortably from a few feet away and felt the beads of sweat start to form on his forehead. This was going to be more difficult than he anticipated. Perhaps he should have left this task with Bran after all, he thought to himself.
Jon turned back to Sam, his gaze as intense as ever. "You were saying…"
Sam cleared his throat. There was nothing for it; he would just have to tell them both.
"I believe… that is we believe, Bran and I, that we know who your mother is… Was."
Jon sat back in his chair and frowned. "How?" He asked.
"Well, you know Bran can see things now… the three eyed raven, whatever that means." Sam said hesitatingly, thinking the words out, "And well, some of the things he's seen… they concern you. And I've been doing a bit of reading about our recent history and it all seems to… fit.
"What are you talking about Sam?" Jon said half-exasperated, half-amused.
"I mean…" Sam said, flustered, "Its not just about your mother, its your father too."
"My father?"
Sam nodded and held his hand up to stop Jon as he opened his mouth to speak again. Sam took a deep breath. "You are half Stark but not on your fathers side, it's on your mothers. Your mother was Lyanna Stark, Lord Eddard's sister," Sam said in one quick breath.
Jon watched Sam in confusion, his brow furrowed. His friend was mistaken.
"That impossible Sam," He said.
"I know it sounds a little mad, but just hear me out…-" Sam started but was cut off
"Lord St- My father wouldn't lie about something like that," Jon said definitively, "You didn't know him, but he wouldn't."
"Not in normal circumstances, no," Sam said, slowly, "But if he didn't have any choice… If it was the only wa-
"You don't understand," Jon said, standing up in frustration, causing Ghost to raise his head and growl softly, "His own wife hated me Sam. She despised me for being her husband's bastard. If I were really his sister's child, why would he lie to her? To me?"
"Because it was the only way to protect you," Sam said, trying to explain.
"Protect me from what?" Jon asked, infuriated now.
"King Robert, The Usurper." Daenerys voice cut through their disagreement like ice. Jon had almost forgot that she was there. She sat quietly in her chair, her eyes on the flickering yellow of the flames. Her face was expressionless and she didn't look up.
Jon wasn't sure why, but he felt a sudden slow creep of dread up his spine. He had a terrible sense of foreboding that whatever else Sam had to tell him, he didn't want to hear it. And Daenerys knew it too. There was a long moment of silence as Jon tried to piece together the puzzle it seemed she had already solved.
"Do you remember the story of how Robert's rebellion started, Jon?" Sam prodded lightly, his voice soft.
"Of course I do. Robert turned on the Targaryens after his betrothed was taken by Prince Rhaegar…" Jon muttered staring into the fire, before looking up suddenly in astonishment. "Lyanna Stark was his betrothed and… Prince Rhaegar kidnapped her."
"My brother had a kind heart," Daenerys said softly, "He didn't kidnap anyone. He didn't rape anyone."
Jon watched Daenerys uncertainly and then turned back to Sam who gave a small nod in agreement. They had loved each other.
"She was pregnant?" Jon asked. Sam nodded again.
Jon turned and walked a few step away from them and the circle of firelight. He ran a hand through his hair, his brow knotted. This was too much to process. Too many repercussions to untangle in a single sitting.
"So I'm not a Stark bastard," he muttered, "I'm a…"
"A Targaryen," Daenerys said, "Still a bastard, but a Targaryen one."
Jon swallowed and looked over to her. Her face was soft and sad. It was as if he could feel the chasm tearing the two of them apart, the revelations pushing her slowly away from him until he felt he was staring at her from across a great divide. So many repercussions...
"If King Robert had known you were alive, he would have never stopped hunting you," she said quietly, "Lord Eddard Stark lied to his King to protect you."
Jon looked away. He moved towards the window and leant against the cold stone of the windowsill, his eyes on the dark winter sky. Ghost got up from his place by the fire and padded over to Jon's side, allowing him to run his hand absentmindedly through the direwolves long white fur. All his years he had believed he was the son of the warden of the north and now he was not. Still a bastard, but now the son of a prince. Still half Stark, but not the half he had thought. This changed everything and nothing.
"There's something else," Sam said quietly.
Jon didn't reply. What else could there be?
"At the Citadel, I came across the record of a secret marriage," Sam said delicately. "Prior to the fall of the Targaryens, Prince Rhaegar had his marriage to Elia Martell annulled. He was remarried in a secret ceremony in Dorne to Lyanna Stark."
"They were married?" Daenerys asked sharply. Jon didn't need to turn around to know Sam nodded.
"So then… He's legitimate." Another nod.
Jon turned back to the room just in time to catch the fire in Daenerys eyes before it was quickly snuffed out. She stood up, her face like ice. They watched each other for a long moment across the room, Daenerys breathing deeply. Jon had no words but he could feel the hole in his chest rapidly expanding and a deep cold emptiness engulfing him.
Daenerys turned to go. She had a hand on the door before she paused and half turned back.
"What did my brother name him?"
Sam swallowed. "Aegon Targaryen, Your Grace."
Another pause and then she was gone. And with one conversation, Jon's world shattered.