What if the Targaryen's rule was not ended by rebellion, what if prince Rhaegar fought against his father with the other rebelling houses and married Cersei Lannnister. This will take place mostly the same time as game of thrones does besides the prologue. However later I may go back and write a prequel to this story about young Ned and Rhaegar and everything leading up to when Game of thrones starts.
Prologue
Prince Rhaegar knew of his father's madness and could ignore it no longer, he started the secret 'plot' as he supposed vile men would call it with his own mother whom agreed it was time to end Aerys II's rule before things got more out of hand. Only a month before the Tournament he would use to gain the strength of his lords, his beloved wife died, her third pregnancy that just began was to much on her. "A terrible tragedy no doubt, an opportune one though." The queen told her eldest son as she whipped his tears away in her chambers once they were alone. "Now you have your own marriage to offer as well as that off your children and brother Visery's and your brother yet to come." She told him looking from the sleeping little toddler on her bed, she liked to keep him close and far from his father. Then she gestured to her stomach filled with her next babe.
"Babies, one not even yet born, we can hardly offer their hands in marriage." Rhaegar sighed.
"Lord Lannister offered his daughters hand to you when you were a mere boy on the first week of her life. Everyone wants to marry a Targaryen, I'm not suggesting they marry tomorrow but perhaps you could remind them that the future is coming with a handful of strong good Targaryen's and that if they stand with us now we will stand with them."
"Yes mother." Rhaegar said respectfully he knew his mother was much more then a woman who struggled to bare children as she was seen to be, she was Targaryen daughter, she was blood of the dragon and cunning.
"It wouldn't hurt if you stood with the Lannister girl someday soon." She said gaging her sons quick reaction.
"No, no. What about the Stark girl? She's…. pretty." He said putting it quiet mildly.
"And promised to the young ill-tempered Baratheon Lord, we need him. I know it's unfair to ask of you to put your heart aside but dear son-" She started he got up to leave but she grabbed his hand pulling him back to her. "You have always been weary of it beloved son, but you are the prince who was promised, don't you see! It is not your destiny to fight an old fisherwives tale in the north, you will lead your people through the long night that is your fathers gruesome reign, you who was born of salt and smoke at Summer hall, this is your destiny son, put it above any girl." She wisely advised.
He did as he was told and used the tournament for allies only to find the Lords were going to rise up with or without him. That was why Catelyn Tully would marry Bryden Stark, that's why Lysa Tully would marry Jon Arryn and that's why beautiful Lyanna Stark would marry Robert Baratheon. They meet in a private room at Harranhall at the prince's request.
"Of course, we were going to insert you the rightful ruler as king, we just couldn't be certain you would stand with us and not your father." Rickard Stark told him kindly, with him were his two elder boys as his youngest son and daughter were some of their many look outs.
On Robbert Baratheon's face it was clear to see he wanted to say, what man wouldn't stand behind his father.
"My father is sick, he grows paranoid and violent every day, I cannot kill him for he is my father, but with your help I will be inserted as Prince Regent until he passes." He said eloquently with a respectful nod to lord Stark.
"Will the Dornish stand with you or your father?" Jon Arryn was the next man to speak in the darkened room lit with only one candle, he presumed they men in here were to scared to even let the gods know what they are planning yet.
"I can't be certain before Elia died they would most certainly fight for their princess." Rhaegar admitted.
"You will have to remind them your daughter is a princess of seven kingdoms including Dorne, just as your son and heir is half dornish." Jon said wisely.
"Elia wrote this to her brother before she passed, I will send it with a letter of my own under my seal, I hope it's enough." He said passing it to Jon who read it and smiled before passing it to Ned who then passed it to Robbert Baratheon who only glanced at it before handing it back and the Targaryen prince tucked it back safely in his pocket.
"That should work shouldn't it Jon!" Robbert gleefully asked the lord of the vale as if he was still his young ward.
"Yes, I am so sorry for your loss prince, you are so young to be morning a wife but know she is protecting her husband and children even now from the grave." Jon said much more respectfully.
"Then I pray she forgives me for taking a new wife to concrete our alliance, just as you are doing, I want to make sure we are all in this together." Rhaegar said and they knew exactly what he meant these marriages insured nobody could leave the others high and dry.
"We will fight together, and if necessary die together." Brandon Stark said giving the prince a small smile, he was grateful, he in all his royal glory was the outsider in this room. Brandon made him feel as though he was not a friendless outsider.
"That's very reasonable my prince-" Jon Ayrrn said before being interrupted by Robbert.
"Whom is he to marry? The Tully's are promised, Lyanna is promised to me, is he to marry one of my brothers!?" Robbert asked showing that temper.
"Lord Robbert please, I will give up my bride, as long as Lord stark agrees to marry his son to the second Tully and the prince can take the first as his own." Jon said simply, and Rickard Stark nodded his agreement. Brandon tried to hide his disappointment as a raised nobleman instead of acting like a brute as Robbert Baratheon did.
"I am not here to steal the wife of any man. Tywin Lannister has long wanted me to Marry his daughter, my mother will arrange it and Lord Tywin will agree to bankroll the rebellion, mother says he will want a wife for his son and heir Jamie. He will have to see daughters are something we are quite short of, he will come to our side." Rhaegar said he saw the glee in all their faces all of them working together could easily do this great thing even if it does come to war. And it showed them that he is a good prince willing to make sacrifices for them, his lords.
"The gods are good." Jon Arryn said softly.
He knew not just how good they were, that night the king angered Lord Lannister for the last time taking Jamie into his kingsguard, Tywin quit his job and joined the rebellion.
They hoped king Aery's would go easy with his son asking him to, in a letter of course they couldn't risk the prince dying at the capital, Queen Rhaella saw to it that his children and hers were already gone with her to dragonstone protected by his men. Aerys did not give in as they had hoped. Since he had another son he ordered the death of his first born but with the North, Vale, Riverlands, and Westerlands against him it was a very short war.
It was not without death, Brandon Stark died lured to Kingslanding by a fake letter from his dear friend and prince he was brutally murdered by Aerys and Prince Rhaegar wept for his dear friend, he now knew even if they called him kingslayer, his father had to die. Through his grief he and Ned Stark became brothers and he even learned to like the brute robbert Baratheon as the three waged their war. After the death of his eldest son lord Rickard died of grief and Jon Ayrrn told Ned he had to marry Catelyn Tully in his brother's place.
Rhaegar would be happy to marry quiet sweet Catelyn, he knew not of Cersei who he was now promised to, but he had a deep dislike for her father who was his fathers greatest friend until it no longer suited him. He assumed their friendship would last just as long. Until it no longer suited Tywin.
Rhaegar was declared the true king and with that the kings guard who adored their prince took their old king as prisoner waiting for Rhaegar and his friends to finish the war at the trident made up of soldiers from Dorne who disapproved of the prince's engagement and soldiers from the reach and Kingslanding. Robbert stayed behind hurt from the battle Rhaegar and Ned arrived at the capital to see Tywin Lannisters good work and Tywin's son in the throne room sitting on the throne with Rhaegar's father dead on the floor.
Ned approved as his friend threw Jamie Lannister the kingslayer into a cell, but Tywin had his son out of the cell before he even arrived at Kingslanding with Cersei.
House Tyrell with the rest of the reach begged forgiveness and it was given and Dorne came back into the fold as well when Rhaegar promised them that Aegon would not be set aside for any child he fathered from the Lannister girl. The Lannister's were outraged and Rhaegar found himself in a cold marriage.
The last death of the war was that of Rhaegar' s own mother. She died giving birth to a baby girl. All four of the royal Targaryen's were brought back to Kingslanding to be raised together by Rhaegar and his wife. Each set of siblings had a boy and a girl, many thought they'd marry each other as tradition but Rhaegar had already promised the future to the lords of Westeros, perhaps with the death of this tradition there would be peace in the realm, but he doubted as much.