The Dragon has Three Heads

Author's Note: This idea has been running around for me and wouldn't stop until I wrote it out. This will be a rather fast paced story as things unfold. Also, it is a strictly Jon/Dany fic.

Chapter One

Lord Eddard Stark of Winterfell was worried. His lady wife Catelyn had just brought him word that his foster-father Jon Arryn, Lord of the Vale and Hand of the King, was dead. Not only that, but King Robert Baratheon was on his way to Winterfell. along with the entire court. No doubt it was to ask that he assume the position of Hand on the Small Council. Although the idea of him being in that viper's pit in Kings Landing disturbed him, that was not what truly had him worried. No, he was worried for an entirely different reason; one which very few people knew. It all centered around his so-called bastard son Jon Snow.

Though it pained him greatly, Ned was going to have to tell the boy the truth; Catelyn as well, as she deserved to know. He had known he would be unable to keep the secret indefinitely. He prayed the boy would understand for he truly loved him as if he were his own son. He would not allow him to go to the Wall before he had even truly lived. He would have to go to Howland Reed's with the others. It would only take one look at his deep violet eyes for Robert to realize whose son he was. Catelyn interrupted his musings.

"Ned, what is the matter. I realize this news is unfortunate, but something else is troubling you, I can tell," she said.

"Cat, meet me in my solar, I have much to discuss with you," he told her.

She could sense the absolute seriousness in his tone and realized something else entirely was going on. She wanted to demand answers in that moment, but realized Ned would not be forced.

"As you will husband, I shall see you there directly," she said.

With that she walked off and Ned braced himself to reveal his darkest secrets to two of the people he loved the most. After leaving the godswood he located Jon sparring in the practice yard sparring with Robb. After beckoning him to follow they set off for his solar. He regretted that what he would tell the boy would turn his world upside down, but there was no other way. They entered his solar and he saw Catelyn get that look on her face she always did in Jon's presence. Seeing the look on his own face however she held her tongue. He steeled his resolve as he collected some of the documents he had in his possesion relating to Jon.

"Jon, Catelyn, what I am about to reveal to you cannot be shared with anyone else. It is of the utmost importance. If the wrong people found out it could mean all our heads on spikes. I would have your words," he told them.

Jon promised, "You have my word Lord Stark."

"And mine as well husband," said Catelyn.

Ned began, "alright, first off you must understand that I had always had my suspicions about what truly happend to my sister. I knew Lyanna had no desire to wed Robert Baratheon. She was always so fierce and strong. She knew all about Robert, and would not subject herself to that kind of married life. I should have tried to force my father to break their betrothal, but was too blinded by my friendship with Robert. I should have looked out for my little sister's interests first and foremost. But, I didn't and I hold no ill-will to her for thinking to save herself."

"Lyanna was not kidnapped. She went with Prince Rhaegar willingly. She was married before the heart tree here in Winterfell, and again in the sept on Dragonstone in the presence of some members of the Kingsguard and Queen Rhaella. Pricess Elia was aware of this and had them go to the Tower of Joy in the Red Mountains of Dorne to hide. She had been told she would die if she were to have another child. As he wanted a third child and she couldn't give him one, she gave them her blessing. Their marriage was political and they were friends, but nothing more."

"Ned, what does this have to do with anything?" Catelyn asked, although she had a sneaking suspision looking at the violet eyes of her husband's supposed bastard.

"You'll understand in a moment," he promised.

"When the rebellion was all but over and I went to find my sister in Dorne, certain events occurred that I lied about. I found the tower guarded by Ser Arthur Dayne, Ser Oswell Whent, and the Lord Commander of the Kingsguard Ser Gerold Hightower. Varys the eunuch had sent word to them for them to allow me entrance. There was no fight to the death. I found my sister inside the tower. She was weak from blood loss, but she was not dying."

"What?" both Jon and Catelyn exclaimed.

"She was recovering from childbirth. She had bore a son to Prince Rhaegar several weeks previously. He had curly black hair and violet eyes," he explained.

"Me," Jon said.

"Was it me?" he asked.

"Yes, Jon. You are my sister's child from her husband Prince Rhaegar. You have to understand Jon, Catelyn; the sack of Kings Landing had already occurred. I saw the man I once considered my best friend smile down at the corpses that Tywin Lannister presented to Robert as he called them 'dragonspawn'. He would have killed you Jon in a heart beat. Robert did not know it, but the reason the finest of the Targaryen Kingsguard was at that tower was because they were protecting their king. When word was sent by them of your birth to Dragonstone, your grandmother Queen Rhaella had you immediately proclaimed king."

Ned handed Catelyn and Jon some parchment bearing the seal of House Targaryen. They saw right their in writing the proclamation by Queen Rhaella of King Jaehaerys III Targaryen, King of the Andals and the Rhoynar and of the First Men, Lord of the Seven Kingdoms. He could see both of their heads were spinning and he hadn't even told them the whole truth yet.

"Lyanna refused to let Robert have her, and after seeing the true side of him I could hardly blame her. Howland Reed of Greywater Watch offered to hide all of them with him in the Neck. No one would find them there he had promised." Ned told them.

"Then why didn't I grow up there? If this is all real, why did my mother send me to you?" Jon asked.

"I'll answer that in a moment," Ned told him.

"The was another child already in the tower when I got there," he said.

"Who?" asked Catelyn.

"It was your sister Jon, the Princess Rhaenys," Ned said.

"How, I thought she was killed by Ser Amory Lorch?" Jon asked with hope beginning to bloom in his chest. He didn't care that he was apparently a king and had been all of his life. He only cared that even if Robb and the others weren't his real brothers and sisters, (although they always would be to him) he did have a true sibling out there in the world.

"She was saved by Varys. He searched for and found a replacement that looked similar enough to the princess the moment he heard Rhaegar had fallen. That was the child the Tywin Lannister's beast killed. He was unable to find a babe to replace baby Aegon as the Mad King was keeping him around him and guarded constantly as a hostage. Aerys didn't care what happend to Rhaenys. She was swapped and sent to the Tower of Joy to be protected by the loyal Kingsguard."

"Jon, your safety was of paramount importance to all of them. All of their hopes rested on you. Lyanna and I however were more concerned with you having a happy and normal childhood. You would never have that hidden away with them and from the rest of the world. Also, should they ever be discovered, you would be immediately killed. We decided that for your own happiness and safety, I would claim you as mine own bastard son. You look enough like your mother that noone from here ever noticed. I allowed the rumour to circulate, that based on your eyes, Ashara Dayne was your mother. Please understand Jon, that your mother and I only wanted you to be safe and happy." He implored Jon to understand before looking his wife in the eye.

"I know I have hurt you with this lie Cat, but when I first came back I had only truly known you for barely the week we spent together before I left for the war. Of course, I soon realized that I could trust you completely, but I if we were ever discovered I couldn't risk that you or our children would come to harm. If you didn't know, no one could harm you. I couldn't risk our family Cat," he told her sincerely.

Catelyn was silent for a moment as was Jon. Both were lost in their own thoughts and feeling somewhat betrayed. But looking into Ned's eyes beseeching them to understand, they both let themselves truly think about the situation he had found himself in through no fault of his own.

After a while Catelyn replied, "I understand my lord. I don't like that I was lied to, but I understand."

She shifted in her seat and looked at her husband's nephew. She felt so much guilt for how she had treated him. She could have...should have, she told herself; treated him so much better. Shame welled within her as she determined then and there to do what she could to make up for her actions.

"Jon," she said, calling him by his name for one of the first times in years.

"I need to apologize to you. I never should have treated you as I have. I did try, so hard sometimes to be different, to look at you differently. I can only tell you that I only thought Ned's refusal to tell me who your mother was and the fact that he raised you here and even had special tutors for you like Ser Geris, who i now suspect is actually Ser Gerold Hightower, that I knew were not really meant for Robb as well. I thought it was all because he loved Ashara Dayne so much that he regretted our marriage and was trying to make it up to her by raising you like that. Every time I saw you that was all I could think about; how I could never hold his heart like she had. If I had known you were really my nephew, I swear to you I would have raised you as my own child. I hope you can find it in yourself to forgive my foolishness, and I am sorry," Catelyn told Jon.

Jon sat their stunned utterly. Never did he think Lady Catelyn would ever speak to him like that. He sat their thinking over her words. He knew he was treated differently by Lord Stark than anyone else in his former position. He could understand why Lady Catelyn would think the way she did. Yes, her treatment of him had hurt him, but he now understood her better. He could not find it in himself to hate her. She was as much a victim in this deception as him. It would have looked strange indeed if she had treated him better than with mere civility. That was probably one reason his apparent uncle hadn't told her the truth. It would have been very suspicious.

"My lady, I thank you and I harbour you no ill-will. I understand, and I am sorry to have been the cause of so much pain to you. I always respected you a great deal," Jon told her.

Catelyn had a tear in her eye as she did something that was a first for Jon. She leaned over and embraced him in her arms. He hugged her back and he whispered a "thank you" to her.

Ned couldn't describe how happy the sight before him made him. He had longed to tell his beloved wife the truth for many years now. When the two broke apart he brought them back to the matter at hand.

"With Robert Baratheon on his way here, you must leave Jon. If Robert saw you or even some of his court, you could be recognized as Prince Rhaegar's son fairly easily. I don't want you going to the Wall or any other nonsense like that. You are only ten and four name days and still have your whole life before you. I want you to go stay with you mother and sister in the Neck at Greywater Watch," he told him.

"Cat you were also right. Ser Geris is truly Ser Gerold Hightower. He will escort you there. Ser Arthur Dayne and his sister Ashara are hidden away there as well. Lady Ashara is actually married to Lord Howland and has two children with him. She and you mother Lyanna have raised your sister Rhaenys. You were always meant to go eventually, and it's time you got to know your mother and sister," Ned explained.

"I can hardly believe all of this is real. It seems more like some sort of fairy tale," said Jon.

"It is very real, and very dangerous," Ned told him.

"You are the True King of Westeros. There is something else you both should know. Jon Arryn knew about you as well. He found out when you were very young. He helped along with Lord Varys to keep the secret. He knew what Robert and the Lannisters would do. If anything ever happens, certain lords of the Vale have sworn to help protect all of you and even fight for you if the Lannisters try anything," he told them.

"They will also have the support of House Tully and the might of the Riverlands if needs be," Catelyn swore.

"Family, Duty, and Honour," she said to them.