A/N: So here is my first fanfic! I hope you guys like the story, and this idea has been on my mind for awhile now. It is an AU about what would have happened had Rhaegar and Lyanna survived Robert's Rebellion. We will see Jon grow up alongside Viserys and Daenerys, and him coming into contact with his Stark family down the road. I hope you enjoy.

Disclaimer: I don't own any of these characters. All credit goes to George R.R. Martin.

Chapter 1 Rhaegar

The killed another Rhaegar on the Trident, Rhaegar thought, The Usurper killed another man. The new King of Westeros stood there in what used to be his father's chambers in Maegor's Holdfast, as he sat there and watched his wife nurse his son. The chamber was a mess when he first stumbled upon it, but he had the place cleaned up. Rhaegar of all people knew of his father's curiosity with fire, and was privy to his growing madness at first hand. If he hadn't killed Brandon or Rickard Stark, if Rhaegar hadn't…That is behind us now.

Rhaegar turned his attention back to his new wife: Lyanna Stark. His wife sat there in a white dress, as she nursed their newborn babe. Jon, what a weird name for a Targaryen. Lyanna noticed his gaze and she smiled at him, as she turned her attention back to Jon. The babe was suckling at her breast and it caused Rhaegar's heart to swell, but it also caused much sadness in his heart. Elia, Rhaenys, Aegon. His wife had been killed by the men of Tywin Lannister, and Rhaegar had to hear about how they did it. Tywin had given him the heads of Gregor Clegane and Amory Loch, as compensation. As if that would be enough compensation for the murder of his wife and children. What man would do that to a little girl, or a newborn babe? He shook the thoughts off, and wished for his harp as he noticed Lyanna had seen his look of sorrow.

"What is wrong?" She asked, tilting Jon's head up as he was feeding.

"Nothing," he replied, smiling. Lyanna could tell when he was lying.

"Liar." She said. "I can tell when something is wrong, Rhaegar. Tell me."

He sighed. "I was just thinking about, Elia."

Thoughts of his former wife, and children forever on his mind.

"I'm sorry," Lyanna replied. "What happened to her was horrible, as what they did to Rhaenys and Aegon. I'm so sorry, Aegon."

"At least Tywin Lannister had the decency to hand me their heads. He says that he did not command them to do such, but I know he did."

Once word had spread through Westeros that Rhaegar had supposedly been killed, he knew that was when Tywin would come out of hiding. Rhaegar was planning on going to the Trident to face off with the Usurper once and for all, but Barristan had convinced him otherwise, telling him that King's Landing and his father needed him; forcing him to stay behind. So, they made another knight similar in Rhaegar's stature dawn his armor on the Trident. Once the news came, he knew he couldn't wait any longer. So, he met up with whatever loyalists forces were left and came up from behind on Tywin's forces. He drove the man from King's Landing, and let the man retreat back to Casterly Rock. It was when he found his wife and daughter in crimson cloaks on the floor of the Great Hall, with a smirking Jaime Lannister on the Iron Throne standing above his fathers dead body that he knew he had truly lost.

It was then that the burp that came from his son stirred him from his thoughts.

"You mustn't blame yourself, Rhaegar." Lyanna said, as she padded the babes back.

"Who else could I blame? If I had just gone to the Trident and killed Robert myself, if we didn't…"

"What you did or didn't do is now in the past. One mustn't dwell on roads you could have followed."

Rhaegar laughed. "Mayhaps you're right, Lyanna. But I shall feel this guilt until the day I die, I fear."

"It is Robert you should place the blame on."

"Robert," Rhaegar cursed under his breath.

"It is he who raised his banners for me! And it is he who caused all these problems. Not you."

Rhaegar sighed. "So I have been telling myself as of late, so sleep can come easier."

"It is the truth, Rhaegar. Nothing more."

The Usurper had gotten wind about the true Rhaegar finally showing himself, and he had tried to come down on King's Landing with his army. The siege lasted for a little while, but finally the Martells came and relieved the city. Defeating Robert and the remnants of his army. Once the man knew that everything was lost he fled across the Narrow Sea, and left Storm's End in the hands of his younger brother, Stannis. Now the man was the Lord of Storm's End and bent the knee like Jon Arryn and everyone else. Rhaegar had pardoned every man who swore an oath of fealty.

Jaime Lannister was now currently on his way to the Wall, as befitting a murderer and Kingslayer, but perhaps it was for the best what happened to Aerys. Rhaegar didn't know. Jaime had told Rhaegar that he had killed Aerys for the good of King's Landing, and the realm. That Aerys had planned on burning the city to the ground with wildfire. It was then that Tywin had come into the city. The Night's Watch will be a good enough punishment, Rhaegar thought. He knew that the Watch was deteriorating by the year, and was now just a band of boys, rapers, and thieves. It will be enough punishment for a man who could have been the heir to House Lannister, and Warden of the West. Now, word had just reached him that the Kingslayers party had been attacked on the Kingsroad, and his royal escorts had been killed. The man himself had gone missing. Lyanna figured Tywin had something to do with it, but nobody knew.

"Will your brother swear fealty?" Rhaegar heard himself ask.

Lyanna looked up at him, as Jon had fallen asleep in her arms. "Yes. Ned will swear an oath of fealty. He is my brother and wouldn't go against me."

"Are you sure?"

"Of course!" She re-assured. "Why wouldn't he? Ned loves me, Rhaegar. The man would do anything for me. You saw that at the Tower of Joy."

"That battle cost the lives of too many good men."

"I'm sorry about Arthur. I know he was a good friend to you."

"Arthur died doing his duty, as any knight should."

"I remember meeting him at the Tourney of Harrenhal. He let me hold Dawn, what a sword that was! The balance and length. It was light as a feather!"

Rhaegar laughed at his wife's intrigue with swords. She'd probably carry one around if I let her. Lyanna, was very well skilled at a blade and could probably best Rhaegar in combat.

"Where will Ned go now?" Rhaegar asked.

"Ned will go back to Riverrun, Rhaegar. It is there that he will meet up with Catelyn and go back to Winterfell."

"I figured that."

Lyanna scoffed. "Then why did you ask?"

He shrugged. "I'm not sure."

"Look my brother will be loyal to you. I know he helped Robert out in the rebellion, but that was because of what happened to my father and Brandon. Not to mention that Robert was his childhood friend. Ned will be loyal."

Rhaegar knew in the back of his mind that Ned Stark would serve the realm faithfully, and would guard the North for him. He was ever faithful to Lyanna, and would do anything for her. It was her that stayed any further punishment upon the Starks, such as receiving a ward from them.

"I know," Rhaegar said, "I know he will."

"I just can't wait for Jon to meet them one day," said Lyanna, the smile clear on her face. "Ned will love, Jon. I know it."

"Does Ned have a child of his own?"

Lyanna nodded. "Yes. He told me that Catelyn was with child, and that she should probably have given birth by now."

"That is good to hear."

"We have to visit them at Winterfell," Lyanna insisted.

"And we will," replied Rhaegar, "when the time is right. I have many things to do before we can consider that."

Rhaegar had fallen in love with Lyanna at the Tourney of Harrenhal. He remembered seeing the dark haired Stark woman, and was immediately attracted to her beauty. A wild beauty, he figured to himself, but there was something different about her. Elia, was a good wife and mother, she was smart, gracious, and overall a good person. Rhaegar still felt shames sting for his betrayal of Elia, but he seemed to have fallen for Lyanna. The dragon has three-heads. It was there at Harrenhal that he found out Lyanna was the mysterious Knight of the Laughing Tree, and confronted her about it. They began to spend more time together, in secret, since then and fell for each other. And when Rhaegar won it all he crowned her the Queen of Love and Beauty. They got married in secret getting the same Septon who had married his mother and father, and then he spirited her away to Dorne.

Rhaegar went to the Tower of Joy after Robert's army had been separated and defeated. Once the Usurper was in his Essos and out of sight, Rhaegar made the trip to the middle of Dorne. He knew that Lyanna had gotten with child, and decided that Dorne was the safest place for her. Not only was it a large vast desert that was impossible to track, it would be the last place that Robert would expect. Once he arrived, Rhaegar found the dead bodies of Gerold Hightower, his friend Arthur Dayne, Oswell Whent, and five of Ned Starks companions. He ran upstairs to Lyanna's chambers, and found her there cradling a boy in her arms with Ned Stark and a crannogmen next to him by the name of Howland Reed. From there Ned returned to Starfall with Howland to return Arthur's sword, Dawn. Rhaegar and Lyanna then went to King's Landing with their new child, Jon.

"Why did you name our son, Jon?" Rhaegar asked.

Lyanna shrugged with the sleeping babe in her arms. "I figured it is a nice name."

"You named him after the Lord of the Vale. The man who rose in rebellion with Robert."

Lyanna stared at him with narrow eyes. "No. I named him after an honorable man who has a clear sense of duty and justice. I named him after a man who practically was a second father to my brother. Jon Arryn is a good man, Rhaegar. He will keep to his word."

"It is not Jon Arryn who gives me restless nights."

"Is it Stannis?"

Not Stannis, Rhaegar thought. The newly formed Lord of Storm's End had sworn his fealty once his brother was defeated, and Rhaegar had ordered the siege lifted. He was reluctant to bend, but Rhaegar knew him as a dutiful and honorable man who had a good sense of justice. Although, he was known to be a very serious man. Lyanna and Ned had assured him that they shouldn't worry about Stannis. It was Tywin who gave him restless sleep. Tywin was known for not forgiving a slight, hence the Rains of Castamere being its families song. Rhaegar had sent his only heir to the Wall, forsaking him of any claim to his ancestral home. Which he knew was all Tywin wanted. That, in his eyes, would be punishment in its own, but Jaime had gone missing.

"No, it is Tywin."

Lyanna scoffed. "As it should be. The Rains of Castamere aren't based on myth!"

A knock came on the door, as both Rhaegar and Lyanna stopped talking. He heard the grumbling of a child on the other side and knew it was his younger brother, Viserys. The young boy had been through enough since the start of the rebellion, and Rhaegar knew he had to take care of him.

"Come in."

The door quietly creaked open, as he saw his mother walk in through the door. Queen Rhaella was heavy with child, and could give birth at any moment. Aerys, had sent her away to Dragonstone once he got word of Tywin Lannister sending his army from Casterly Rock. Once, Robert, had been defeated Rhaegar had sent some men to bring her back. He believed she should give birth to her final child in the Red Keep, and not an island of volcanic ash.

"Hello, mother." Rhaegar said.

"Hello, Rhaegar."

Rhaegar noticed his younger brother standing behind her leg, as he bid him to enter with her. He ran over and huddled over his nephew, as Lyanna showed the babe to him. Rhaegar hoped that they would grow up to be close. Rhaella walked over and slowly sat down on a chair next to them.

"How are you doing?" She asked.

Rhaegar sighed. "Just trying to figure out what to do with the remaining rebel forces."

"What are you going to do?"

"Give the opportunity for all of them to swear me oaths of fealty. I know that Ned Stark will be loyal, as will Jon Arryn, and Stannis. However, it is Tywin that makes me worry."

"Tywin…" Rhaella muttered in disgust. "He was such a good man when Joanna was alive. It seemed his better half died with her."

"That is what everyone says," Rhaegar replied. He knew that it was the truth.

"What will you do with, Tywin?" Rhaella asked.

"I have sent his son, Jaime to the Wall for killing my father, but it seems he hit a snag upon the Kingsroad. He has gone missing."

"No doubt, Tywin, had a hand in that."

Rhaegar nodded. "I'm inclined to agree with you. However, if he were to have taken Jaime then I would not let him inherit. Everyone knows that Tywin has always wanted Jaime to be his heir. It is why he never forgave father for letting Jaime join the Kingsguard."

"What about your small council?" Lyanna asked. Still distracting Viserys with the babe.

Rhaegar sighed. "So far it is just me, and Ser Barristan. I'd really like Maester Aemon to become the Grand Maester, but the Citadel decides that. Master of Ships, I was thinking of Mace Tyrell, as a gesture of good faith. I'm thinking to make Lyanna an adviser, and Varys will still be Master of Whisperers. Master of Laws, I don't know yet and neither do I know who to appoint my Hand. If I can't think of anybody then maybe, Tywin."

"Tywin?!" Rhaella exclaimed. "Rhaegar, you can not appoint that man as your Hand of the King!"

"But look how the realm flourished when he was father's hand."

Lyanna scoffed. "That would be an unforgivable slight towards the Martells. They call for Tywin's blood as we speak."

"Lyanna is right," said his mother, "the Martells would see that as a slight. If anything I would recommend, Oberyn Martell."

"Oberyn?"

Rhaella nodded. "Yes, Oberyn. The man was very close to Elia, and the Martells would be kept happy. You know it is the right thing to do. Some of them are still unhappy about…"

She didn't finish, but Rhaegar got the message. Marrying and spiriting, Lyanna, had caused some grievance between him and the Dornish. Oberyn was one to voice his displeasure, but Rhaegar knew he deserved some of it.

"That seems like a good Hand, mother. I will consider it."

A couple of weeks past with nothing really happening. Rhaegar had written to all the high lords in Westeros, proclaiming himself the new king and demanding their oaths of fealty. He had written to Tywin Lannister about his son going missing along the Kingsroad, but the man had not replied. He also wrote to Eddard Stark, Jon Arryn, and Stannis about their pardons provided their oaths were sworn. A raven had been sent to Highgarden informing them about Mace Tyrell being appointed Master of Ships, and he also made sure Arthur's bones were sent to Starfall along with Gerold's and Oswell's.

A bad storm was raging outside, as Rhaegar was sitting in his solar writing to Sunspear. The contents of the raven were of his offer to Oberyn Martell on being the Hand of the King. Rhaegar, was reluctant to ask him, but in some way he knew that his mother was right. He needed to please the Dornish and this was the way to do it. Dragonstone would eventually go to Jon, and it seemed the realm was back in order. He also placed a price on Robert Baratheon's head, dead or alive, and sent the word across Westeros and Essos. Now it is time for peace…

A large crack of lightning resonated across the sky, as it shook the Red Keep. Rhaegar, stood up from his seat and opened the drapes of his window, as he saw the rain drops skidding down the glass. He placed a hand against the window, and kept watching the storm brewing outside. It hadn't rained this bad in awhile, and he figured it was the Gods crying or something. That is when he heard a knock on the door, accompanied by a loud scream.

Rhaegar began to walk over to the door, and opened it. He saw Barristan standing there in his golden armor with his long grey hair, and then he noticed the blood on it.

"Whose blood is that, Ser Barristan?" He asked.

Barristan shook his head. "Something has gone horribly wrong, Your Grace."

"Concerning?"

"It is your mother, Your Grace. Queen Rhaella has given birth, and is now…"

Rhaegar felt his heart sink down to his stomach, as the words were beginning to set in. His mother was going to die in childbirth.

"How much longer?"

"I'm not sure," Barristan swiftly replied. "Not much longer. Rhaella wishes to see you one last time, Rhaegar. She sent me here to escort you."

Rhaegar nodded. "Take me to her."

Barristan nodded at him, and lead Rhaegar down the hall towards the sickroom of Maegor's Holdfast. The sky had turned dark outside due to the storm, and it cast a dark shadow within the hall. The walk there felt like it took three years, and the thunder cracked throughout the Red Keep. Each crack made him wince, because he knew with each step his mother would be closer to death.

Finally, they arrived at the door, as he slowly opened it. His mother was laying down on the bed, her face pale and a pool of blood on the bed, as he saw handmaidens by her side, along with Viserys. That was when he noticed the baby in her arms.

"Rhaegar…" She said in a frail voice.

"Yes, mother." He replied, as he walked over to her side and clutched her hand.

He ordered that Viserys be escorted out of the room, as thinking that a boy so young shouldn't witness death. Rhaella, told him that everything would be alright and that she would see him soon. She gave him one final embrace before turning to Rhaegar, who couldn't keep his eyes off the newborn babe.

"Promise me you'll take care of them, Rhaegar. Promise me you'll take care of Viserys, Jon, and Daenerys."

"Daenerys?"

"Meet your new sister, Rhaegar."

Rhaella gave the babe over to him, as he cradled her in his arms. He looked down at the baby, and noticed it had silver hair with the bright violet Targaryen eyes. A mirror image of his own. Rhaegar knew she would grow to be beautiful.

"Promise me, Rhaegar. Promise me…"

"I promise," he repeated, as his mother smiled.

"Before I die I want you to have something."

"You aren't going to die, mother." Rhaegar urged, as he held the babe.

"Oh my boy…" She said. "Hurry, before it is too late."

"What is it?" He asked.

Rhaella pointed over to a chest that laid on the table, as he looked over at it.

"What is in it?"

"I can't say right now, but make sure you give it to Daenerys when she comes of age. She was meant to have them. Take care of them, Rhaegar. Take…"

Rhaegar stood there with the babe in his arms, as he watched the life flee out of his mother. The woman who had endured giving birth to three children, the woman who had endured his father, the woman who had birthed him and hugged him, and held him when he came to her with a scraped knee. Rhaegar stood there in a trance, as he stared at his mothers lifeless body. He wanted to cry but he couldn't; the tears would not come. Be at peace.

Rhaegar looked down at the child in his arms once more and stared at it. Knowing full well he would keep his mother's promise.

"Hello there," he said staring down at her. "Hello there, Daenerys Stormborn."

A/N: Well there is the first chapter/prologue. Let me know your thoughts.