I've always wondered why Ned allowed Jon to join the Night's Watch before telling him about his mother. It's such a huge life decision. I guess it would've removed a big part of the story, but it never felt right to me. Anyway, this is how I imagined things might go.
Following his father down to the crypts, Jon Snow wondered why the man had chosen this place to have a conversation. I'm not a Stark, he told himself, I don't belong here.
After walking a bit further than Jon had ever dared to go before, Lord Stark stopped and turned around. The candlelight made him look much older than his years, highlighting the silver in his auburn hair and the wrinkles on his features.
"This should be far enough." Father said, looking back towards the entrance. "I doubt anyone will hear us now."
"Why don't you want people to hear us?" Jon knew that Winterfell was packed, and would probably remain so until the king left.
"Jon, what I'm about to say is a secret I've kept since before you were born. Only one other man knows of it, and I'd trust him with my life."
Jon felt a lump in his throat. He must really trust me. Swallowing hard, he nodded and looked up at his father.
"I'd hoped to wait until you were older, but now that you've decided to join the Night's Watch..." Father started, putting a hand on Jon's shoulder. "There are things you must know before you make such a decision. The men of the Night's Watch take a sacred oath before the gods when they join. They forsake lands, titles and family ties." His eyes were sad when he spoke those last words.
"I don't care about any of that. I even told uncle Benjen-"
"I know." Lord Stark interrupted him. "He told me. But you don't know what you'd be giving up."
"And I already have a title." He stared at his father. "I'm the bastard of Winterfell. What family would carry my name?" He asked, failing to keep the scorn from his voice.
"Jon…" The man at least had the decency to look ashamed. He stepped back and glanced away, turning his head from side to side. Is he searching for something? Then his face lit up and he started walking away.
Jon followed, and soon found himself in front of aunt Lyanna's statue.
"She died too young." Lord Stark muttered, putting a hand on the woman's face. Jon still had no idea why they were here, but something unnerved him. Father never talks about Lyanna. "She was a wild one. The wolf blood, my father had called it. Sometimes, I see some of it in Arya…" His face showed something Jon hadn't seen often in his father. Fear.
"Arya's going with you to King's Landing. She'll be safe." Jon said, also trying to convince himself. He loved his little sister. Arya had often been the main reason Winterfell felt like home, despite the best efforts of Lady Stark to make his life miserable.
Lord Stark gave him a weak smile. "Aye, she will." He said, quietly. "But this isn't about her." He took a deep breath. "Jon, it's time I told you about your mother."
Jon's breath was caught in his throat. Ever since he could speak, that had been the single most important thing he wanted to know. Growing up at Winterfell, Lady Stark had made sure he remembered his status. Even Theon Greyjoy hadn't received the same treatment from the Lady of Winterfell. She blames me for being born.
"I'm sorry it took this long, but the memory's still painful." Father started, and Jon felt a strange notion creep into his head. But the man continued, "The last time I saw her, she was dying in a bed of blood." So she's dead, Jon thought, feeling the loss of what he never had. "Childbirth." Father answered the unasked question. "She was too young."
That notion grew too big to ignore, and Jon couldn't help looking at the statue. For the first time, he actually focused on her carved face. She looked a lot like Arya, or what his little sister would look like in a few years.
Suddenly, he remembered a time when Arya had run crying to him. When asked what happened, she told him that Sansa and Jeyne Poole had called her a bastard. That both of them had mentioned how much she looked like Jon and not her mother. Jon had made his little sister laugh when he reminded her that Sansa didn't look much like father either, so maybe she was the bastard. If aunt Lyanna looked like Arya… And Arya looks like me...
It's not possible, he tried to convince himself, but the thought had already taken root. Slowly, he turned his head back towards his father. "Aunt Lyanna…" He croaked hoarsely.
"Is your mother." Lord Stark finished, nodding slowly. "She died giving birth to you, Jon."
"But… that doesn't make sense." Jon couldn't believe his ears. "How could you be my father then?" He asked, trying to remember everything he knew about Lyanna. It wasn't much.
"Lyanna and Rhaegar Targaryen were wedded in a secret ceremony in Dorne." His father's voice was barely higher than a whisper, and he glanced back at the crypt entrance to make sure no one was there. "Most people think the prince had kidnapped and raped her, but that was never true."
"So this Rhaegar is my father…" Jon felt his voice faltering, and a tightening in his chest. His head drooped, his shoulders sagging with the weight of what he had just heard. The one thing he had been sure of, the single source of pride he had in his whole life was being Eddard Stark's son. What am I now?
He felt the man's hands on his shoulders, gripping tight. "I am your father, Jon." He looked up to see two grey eyes staring intently at him. "I raised you as mine own son. Robb, Arya and the others love you as a brother. Nothing is ever going to change that."
My cousins. "This changes everything. Is Jon Snow even my real name?" He asked, still reeling from the information. If my parents were married…
Lord Stark looked uncomfortable. "Lyanna named you Aegon, after the conqueror. But I didn't think it'd be wise. Jon Arryn was like a father to me, so nobody would think twice about that."
"I'm Aegon Targaryen…" That didn't sound right, Jon thought, but at least I'm not a bastard.
"You're still the son of a Stark." The man offered. "My sister made me promise to keep you safe. To protect you from Robert's fury. The king would've killed you and any Targaryen he could get his hands on." He paused for a moment, his eyes unfocused. "I still remember Tywin Lannister presenting the corpses of your siblings to Robert. And his reaction. Dragonspawn, he called them." He went quiet after that, probably lost in thought.
Jon also had to think about this. But there were so many questions. And he's about to leave for King's Landing. Something told him he couldn't write about any of this, so whatever he needed to ask he should ask immediately.
"Before, you said only one other man knew of this. Who?"
"Howland Reed, the lord of Greywater Watch. We were the only survivors of the fight at the Tower of Joy." He answered in a sad tone, but that had only raised more questions.
"There was a fight?" Jon needed to know every detail.
"Aye. Rhaegar had left Lyanna guarded by two kingsguard, Lord Commander Gerold Hightower and Ser Arthur Dayne." He hesitated, before continuing, "They were… unreasonable." Jon waited for more details, but none came.
Hearing those names made him remember something. "What about lady Ashara Dayne? I once overheard the household staff talking about her in hushed whispers, glancing at me."
He looked a little annoyed. "I'd hoped to put an end to those rumors, but I suppose that was wishful thinking…" He said, more to himself, before facing Jon. "Lady Ashara and I were… Well, this was before Brandon's death. Before I even met Catelyn." The man looked guilty. Of what? But he continued, "After I'd found Lyanna, I went to Starfall to return the ancestral blade Dawn back to the Daynes. Lady Ashara had welcomed me with a smile, but I left her in tears." He went quiet again. That didn't answer much, but Jon decided to let it go. Something else sparked his attention.
"Lady Stark doesn't know about me, does she?" Jon asked, fully confident in the answer.
"No." He replied, quietly. "I couldn't risk your life on the chance that she treated you differently. I'm sorry."
Jon shook his head. "You don't have to apologize." He said, but wondered just how differently he would have been treated by the woman had she known all along. Hopefully she wouldn't have been such a...
"I know she hasn't treated you well, Jon. I imagine she blames me, though as her husband she couldn't very well live by my side while hating me. So she shifted the blame to you, an innocent child." He couldn't keep the disappointment from his voice. Did he really expect his wife to love his bastard? He's always expecting the best of people…
"But why, though?" Jon asked, finally.
"Why what?"
"Why did everybody think Rhaegar had kidnapped Lyanna? Why did uncle Brandon ride to King's Landing demanding a fight? Why was the marriage a secret in the first place?" Jon tried to understand. None of this makes any sense if you think about it for too long. "What were they thinking?"
Lord Stark sighed deeply. "I don't have all the answers, Jon. What I do know is that it was a confusing time. The Mad King had alienated half the realm, and there were rumors that Rhaegar planned to depose him. The tourney at Harrenhal was originally intended to gather all lords on the prince's side, but Aerys had discovered the plot and made an appearance. Then Rhaegar won the joust, crowing Lyanna as the queen of love and beauty."
"Wasn't he married?" Jon didn't know much, but that was common knowledge.
"Aye, to Elia Martell." He nodded. "That's another complication. Who knows how the Dornish would've reacted to Rhaegar spurning his wife for Lyanna? But to answer your original question, I have no idea what they were thinking."
I could have been a prince. "So that's why you were worried about me joining the Night's Watch…"
He nodded. "Now you know. If you still want to join, it's an honorable choice, son. Benjen will look after you until you learn to look after yourself. And Robert's wrath won't find you there."
Robert Baratheon killed my father, Jon thought, but he's the best friend of my other father.
"Are there any other living Targaryens?" Jon asked. He remembered hearing something about one of them in Essos, but nothing certain.
Lord Stark hesitated. "Rhaegar's siblings, Viserys and Daenerys, had managed to escape Stannis when he attacked Dragonstone. The last I've heard, they were living in poverty in Essos, fleeing from Robert's assassins and moving from city to city." So that's what would've happened to me, Jon mused. But the man continued, "And there's old Aemon Targaryen, a maester of the Night's Watch. Benjen tells me he's blind and frail, but his mind is still sharp."
Jon considered for a moment. He had wanted to join the Night's Watch because he was a bastard. He had no real choice. Where else could a bastard not be judged for being baseborn? When a man joins the Watch, all his past crimes are forgiven. I thought my crime was being born. But he wasn't a Snow, he was a Targaryen. Was that a crime too?
"Maybe I should speak to this maester Aemon before I decide what to do."
The man nodded, apparently pleased with his decision. "Very well. Just remember what I said about the king. He won't rest until all Targaryens are either dead or beyond his reach. So be careful." He patted Jon on the shoulder and started walking away. "Shall we return?"
Jon looked at the statue again. "I think I'll stay a bit longer." I'm not a Stark, but my mother was.
He smiled and made to leave. When he had reached the stairs, Jon called out, "Lord Stark!" He turned around, with a frown on his face. "I just wanted to say…" Jon swallowed the lump in his throat, then continued, "Th-Thank you… for being my father."
Wow, that got emotional in the end… Some explanations: for the Tower of Joy fight, I used the HBO version because it's more recent. The Ashara/Ned relationship is still clouded by misinformation, so I tried to keep it as vague as possible. I only added it to keep my options open in the future. I wrote an outline for the rest of this story (it involves Jon meeting Daenerys and Viserys), but reading back it's a pretty good one-shot. I'll think about it.
UPDATE: Thought about it. I'll keep it as a one-shot for now.