Chapter 1: Jon
This story mostly follows the book universe, but borrows a few things from the tv series as well. It takes place after the fifth book and sixth season. There will most likely be spoilers for both though this story is very very au so I doubt it will be noticeable unless you know what to look for. Also I haven't actually watched season six yet, I just know what happens in it so this story definitely won't match up very well with it.
Jon Snow knelt on the hard stone floor of the Great Hall in King's Landing. There was not a large gathering of people, only the Queen's most trusted. Jon thought that was well enough, seeing as the large black dragon took up a significant amount of room as it was.
"Jon Snow," He lifted his gaze to meet the violet eyes of the young Targaryen Queen who was seated in the Iron Throne. "I, Daenerys Stormborn of House Targaryen, Mother of Dragons, with these courtiers as witness, pronounce you to be Jon Targaryen, the true son of Rhaegar Targaryen, and King of Westeros. Arise."
And so the boy who was a bastard no longer did, and even the Mother of Dragons bowed her head. Jon was now the third head of the Targaryen dragon, and as Rhaegar's only living child he would rule alongside Daenerys and Aegon Targaryen, though both men knew who held the real power. Jon's face remained impassive as the people in the room dispersed until only he and Daenerys remained. He waited, silent.
"We have but one problem left to face, Jon, and I'm sure you're more aware of it then I."
"Yes, my lady. The matter of the North." It was all the council had been talking about since they had finished securing the South. When Daenerys Stormborn had arrived in Westeros, bringing three dragons and a handful of loyal advisers, to unite forces with Aegon Targaryen who was already well on his way to conquering the Stormlands, not much had stood in her way. With Tywin Lannister dead, Cersei disgraced, and a young boy on the Iron throne, both King's Landing and House Lannister were well on their way to crumbling on their own. All it took was the sight of three dragons flying overhead to convince most of their banner men to abandon ship. Stannis Baratheon's fight had already been finished as well, the man himself dying in the North along with most of his troops. The only trouble they had encountered so far had been from the Tyrells who, after swearing allegiance to the new queen, had promptly begun looking for any possible marriage arrangements. Getting Dorne to swear fealty had been easy as well and their troops had served the Targaryens well in taking over Westeros. Dorne was the strongest, and most certain, ally they had by far, especially considering Aegon had agreed to a marriage with Arianne Martell.
"Yes." The Queen stated after a long moment. "That matter of the North. And the Riverlands as well, though that isn't quite as important. If we can control the North, they should follow peaceably enough."
Jon felt a twinge of anger at that. "The North and the Riverlands only joined the war to get justice against the Lannisters, they never wanted anything to do with your Iron Throne." He stood straighter under her annoyed stare. "My Lady."
Daenerys leaned forward. "That is precisely our problem. They don't want to have anything to do with my kingdom. Helping fight the war against the Lannisters is not the same as supporting the Targaryens. They declared their own King, why should they kneel to us now simply because he's dead? The Riverlands side with the North and the North will fall when the Starks do. I say we execute them. For all their honor let us not forget who aided the Usurper in his quest for the throne, dear nephew." She paused, looking for Jon's reaction.
He did not hide his anger as he thought of the people he had called his family. Only the four youngest still remained. "Whatever the part Lord Eddard Stark played in Robert's Rebellion and its aftermath, he is dead. Along with his wife and his eldest son and heir. All that remain of the Starks are four children, the eldest of which is only fourteen. They had nothing to do with the grievous wrongs done to the Targaryens."
"You would have me spare them when Rhaegar's own children, your brother and sister, were brutally murdered?" Daenerys' voice began but family was not something Jon was willing to back down on.
"My Lady, I fully aware of the fate of the Targaryens, but Lord Stark had nothing to do with the deaths of the innocent children. Call him a fool and a usurper if you will, but Eddard was nothing if not honorable. When the Usurper called for yours and your brother's heads', Stark, the king's own hand, opposed him at risk of treason. I need not remind you that it was Lord Stark who found me, who took me in and raised me as his own son. He hid me from certain death at the hands of his best friend, knowing full well the risks he put on his own wife and son." Jon spared a glance at the Queen and was dismayed to see her face stonier than usual.
"If you kill innocent children who have already been through hell, you will no better than the Usurper, no better than the Mad King who burned his enemies alive, and look what happened to them." Daenerys' temper was rising, as Jon could clearly see. He took a breath. "My Lady, there is no better way to guarantee a full on northern rebellion than by killing House Stark. If nothing else, you must see that. There are other, better, more effective ways to gain their loyalty."
"Without seating a Stark as the Warden of the North?" Daenerys gave Jon a pointed look, then let out a small laugh. "It would almost seem that you preferred being the bastard of Eddard Stark to being a Targaryen, ruler of the Seven Kingdoms." Jon knew better than to rise at her thinly veiled jibe. She sighed and leaned forward. "Tell me then, Your Grace, how would you deal with the Starks."
Jon didn't hesitate. "Sansa Stark and I were the ones who rallied the North to defeat the Boltons and win back Winterfell in the first place. Afterwards, she became Queen Regent of the North until such time as her younger brother, Rickon, was old enough to take over the rule for himself." The process hadn't been quite as smooth as that. There had been many debates over who should rule the North, though surprisingly they were more a result of no one wanting the role, than the reverse. After the horrors Sansa had been through, another marriage and more politics was the last thing she wanted. They had all laughed at the idea of Arya Stark, the wild child and now a hardened killer, ever becoming the Lady of Winterfell. By rights the role should have gone to Bran, but he was the least interested out of all of them, and with his injury, having children and producing an heir was not a possibility. "I know you do not believe me, but the Starks themselves pose you no threat, it's their banner men that are the problem, and the only way to control them is by placing a Stark in control."
The Queen opened her mouth to object, but Jon wasn't finished. "I know you will not stand for that. But what if." Here he hesitated for the first time. He himself was not happy with his own suggestion. "What if you named me the Warden in the North and Lord of Winterfell until Rickon is fit to do it himself. He is still young yet, there are many years until he would rule. In that time we can work on solidifying the North's loyalty without their objection and Rickon could be taught to love the Targaryens. He's nothing but a child now, but in another ten years he could very well be a powerful ally." He left the 'or enemy' unspoken, but he knew the Queen would hear it all the same.
Daenerys didn't react for a long moment and Jon began to grow nervous. When she spoke however, her annoyance had been replaced by a more conversational tone. "I am sure," She said slowly, "that it has not escaped your notice that I have no true claim to the throne as long as you are alive." Jon didn't respond. "Between the two of us and Aegon, only you could hope to gain the support of the North, as a Stark, and you would have the support of Dorne, as Rhaegar's true son. Even the other Houses and the small people, though they will not admit it, would rather see a man raised by the honorable Eddard Stark as ruler of the seven kingdoms rather than an outsider from the East. I have few soldiers and a dragon can only do so much. And yet, here you are asking me to hand you the entirety of the North." Her lips twitched, betraying her humor.
Jon just shook his head. "With all due respect, Your Grace, I do believe the fear and destruction a dragon can bring far outweighs any advantage I may have. You also forget that I have never desired a throne, not in the North and certainly not in this gods forsaken city. Ask of me what you will, but do not make yourself out to be the weaker party."
Daenerys smiled at that, as he had known she would. "Very well, Jon, but these are my conditions. I will let your precious Starks live only because you are so willing to vouch for them. You are a Targaryen and family, whether you like it or not. However," Jon held his breath as the Queen paused before revealing her main condition. "You shall name me your Queen and together we will rule over both the North and South. Also, Bran and Arya shall come and live with us in King's Landing for a while. Sansa and Rickon must remain in Winterfell until you are able to go there yourself, which won't happen until you and I are married. Do you understand?"
Jon gave a curt nod. "Perfectly." And he did. In return for the lives of the children he had once thought of as siblings, Jon Snow would become Jon Targaryen for good, married to the Mother of Dragons. Through him she would have control of the North and her quest for the seven kingdoms of Westeros would be complete.
I'm afraid Daenerys came off as a bit unlikeable/harsh in this, but her entire life she has been struggling to obtain the throne which she sees as her birthright. Also, she doesn't strike me as a person to forgive her enemies easily, especially those who have committed such atrocious crimes against her family. Also this is from Jon's view more or less and he has no particular love for her at the moment.
More will be revealed next chapter. Please R+R :)
