Warning
First time making a Game of Thrones fic. So, I may mess some things up about it, but I'll try my best not to. John Snow will be born a female by the name Visenya. Some events in the timeline might be pushed up or back. There might be some people who suppose to die but lives and vise versa. I will being using information I gather from online lore, Game of Thrones TV show, books, and some fics I read.
Prologue:
281 AC
Robert Baratheon vs Rhaegar Targaryen
Two men were battling it out in the middle of a battlefield with their men. One man dressed in black armor with red markings battled with a shield and sword. Narrowly avoiding a direct from his opponent, it scraped the side of his helmet flinging it off to reveal his white silver hair and angry purple eyes. Returning the swing with a bash of his black with a three headed red dragon shield, he knocked the helmet off the other man. It revealed his short black hair and enraged bright blue eyes. Tightening his grip on his Warhammer and his shield displaying a stag proudly on it.
Both men were fighting for their own reasons but it was curtained on one person. A woman by the name of Lyanna Stark. Robert believed that Rhaegar kidnaped his betrothed and started a war to rescue her. Rhaegar on the other hand took her for multiple reasons. One was to rescue her from a marriage that she didn't want. Second was because of a prophecy he believed in about the prince who was promised. The final reason was because he was in love with her like she was with him. With these reasons they continued to fight. Sword and hammer striking against shields and each other.
The two, each a member of their houses were not alone is this war. Falling underneath the Baratheon banner from the seven kingdoms were the of the North, Vale, and the Riverlands. Underneath the Targaryen banner was the Reach and the Dorne. Robert's hammer smashed into Rhaegar's shield with immense strength forcing back on his feet with a slide.
Ignoring the shakes in pain from the impact Rhaegar leaped up and slammed his sword on his foe's shield forcing him to a knee briefly. The kingdoms joined each side for their own reasons with each one having their own desire. The kingdom in control by the House Lannister called The Westerlands had decided not to declare for either side and wait for a opportunity. The other kingdom run by House Greyjoy had also decided not to join either side. Preferring to watch both sides weaken themselves for their own purpose.
The North, controlled by House Stark had decided to follow Robert due to Rhaegar kidnapping Lyanna. Lord of the house, Rickard Stark and his heir Brandon, traveled down to King's Landing, the capital of the seven kingdoms to demand Lyanna's return and Rhaegar to be punished from the king. The King of the seven kingdoms Aerys Targaryen was not a stable man. Due to multiple events, some unknown and some known like his captured and torture by Lord Darklyn of Duskendale, he started to become mad. Known as the Mad King, he conducted brutal actions, and the burning of people while alive, much to the horror of the people.
When Rickard Stark gave his demand to the King, he was captured and suspended from the rafters, as a fire was lit beneath him by the pyromancers. Rickard was slowly cooked to death in his armor, while his son Brandon, with a tyroshi noose around his neck and a sword just out of his reach, was made to watch his father roast. Reaching for his sword to free his father, he ended up chocking to death. With the capture of his sister and the murder of his father and brother, Eddard Stark assumed Lord of his house and went to war with his brother in all but blood Robert.
With the King demanding the heads of both Robert and Eddard for rebelling, Lord Jon Arryn, paramount of the Vale joined the two in rebellion. He had foster both men when they were young and he treated them as if they were his sons. There was no way he could turn against them, and he saw the perfect opportunity to remove the Mad King from power to stop his madness.
House Tully's Lord, Hoster Tully, ruler of the Riverlands had a betrothal agreement between his daughter Catelyn and Brandon Stark. With Brandon's death House Tully was enraged and agreed to have Eddard take his place while joining in on the war to remove the Mad King.
Rulers of the Reach, House Tyrell, under the lord by the name of Mace Tyrell chose to maintain their loyalty to the Targaryen's and join the war. The Tyrell's owe their rise to power within Highgarden to them and held it despite having a mad king for a ruler. They were still reaping the benefits of that loyalty.
Prince Doran Martell, house lead of House Martell, and ruler of Dorne reluctantly agreed to follow underneath the Targaryen banner during the war. House Martell were able to hold their royal titles due to being able to hold and fight off the Targaryen Conquest, hundreds of years ago. It was only through marriage and agreements that they were brought into the fold. The house was reluctant to join the fight because of the kidnap of Lyanna Stark while he is married to Doran's sister Elia Martell. They must join the fight in order to protect her, her kids, and their power with her being future Queen of the Seven Kingdoms, knowing what will happen if Rhaegar loses this war.
Rhaegar and Robert were locked in even combat, but one was more distracted then the other. Robert's closest friend Eddard had left right before the battle started upon hearing word of Lyanna's location. Taking a small party with him to attract as little attention as possible, they left to The Tower of Joy, within Dorne. With his betrothed on his mind and no answer from Eddard yet, he was worried.
In result it made him make mistakes he shouldn't have. A mistake that cost him dearly when he saw Rhaegar off balance from his last hit with his shield flying off to the side. Instead of going for the assured hit to the man's chest, he swung at the man's head intending to take it clean off.
Seeing the swing coming for his head, allowed Rhaegar to slightly duck underneath the swing, missing him by a hairs breathe. Spinning from the duck he twirled his sword around and slashed Robert deeply across his chest. The sword sliced through metal, leather, cloth, and finally skin, showering a spray of blood as Robert fell to his knees in shock in pain. Following it up, he swung his foot out connecting it hard into his chest, sending Robert flying back into river.
Silence reined out through the battlefield upon seeing Rhaegar win and Robert losing. It was underneath Jon Arryn's leadership that the sound for retreat was called, allowing for the rebel forces to pull back and regroup. Not wanting to purse them at the moment and recover Rhaegar pulled his forces back.
Days had passed since the battle and whether it was from the luck of the Gods or sheer stubbornness, Robert had reemerged back at his forces camp with hastily placed bandages covering his deep wound. The rebellion shouted cheers of joy at his return but as he was being properly treated in his camp, new information was being spread out through the kingdom. Eddard Stark has found his sister Lyanna Stark.
It was good news to hear that he found her but what followed made a wide range of emotions and thoughts spread out through the kingdoms. Lyanna Stark had married Rhaegar Targaryen, becoming his second wife like with Targaryen history and tradition but unfortunately passed away giving birth to Princess Visenya Stark Targaryen. Lyanna explained to Eddard before she passed away that she was never kidnapped but ran away with Rhaegar who she loved. Someone spread the false rumors to incite this war.
With this in mind Eddard wanted to put an end to the war and bring Visenya home with his sister's body, but a issue remained. King Aerys was still in control. With another commander convincing Mace Tyrell to break the siege on the Stormlands capital which is underneath the leadership of House Baratheon but currently controlled by his younger brother Stannis. The Tyrell army moved to regroup with the Targaryen army as the Lannister army had finally made it's move to support the Targaryen's.
With these combined armies and a wounded and distraught Robert, they were not going to win this war without a miracle. Jon convinced Robert to retreat with the idea that he can rebuild and come back stronger then ever. Eddard and the North would be forced to stop fighting due to Eddard and Visenya being under the guard of Lord Commander Gerold Hightower, Ser Oswell Whent, Ser Arthur Dayne, and a few other kingsguard. If he stayed King Aerys will execute them both. If he flees only one of them will die. With a heavy heart and a swear to come back to bring vengeance, Robert fled to Essos with some of his trusted men.
Jon Arryn met with Rhaegar to officially send the surrender of the rebellion and to accept his fate for help leading it. With the two leaders of the rebellion Eddard and Jon brought to King's Landing, the discussion on what to do was discussed.
King Aerys originally wanted to burn both of them like he had done with Rickard but with the combine convincing of his son Rhaegar, his wife Rhaella, Ser Barristan Selmy, and Varys the Master of Whisperers he decided not to. This could lead to more rebellions and headaches when they needed to recover. But he will get his due. He ordered the increase taxes upon the North, Riverlands, Stormlands, and Vale in order to fix the damages and increase his coffers. Robert Baratheon was sentenced to death by a slow fire when they find and capture him (which they haven't). To put the final nail on the coffin upon seeing Visenya's looks being a silver white hair and purple eyes decided that she would stay by his side. If the North and any of its allies decides to rebel again, he will burn the last reminder of Lyanna Stark to death. So now the North had to watch its cohorts in the rebellion and put them down if they start one.
It shattered Eddard's heart having to leave her there in the Mad King's hands. She looked like a copy of his sister Lyanna with Targaryen coloring. But he must do his duty to protect her and the North. Aerys can't live forever and one day he will be reunited with her again. They must be strong.
Robert arriving in Esso's was heartbroken by the lost of his beloved and his exile. But this will not be the end of him. He will not die in this god forsaken desert. He will rise up here and rebuild. Make a stronger and more power army then he ever had before. Then he will return to the seven kingdoms and take it all. He will crush all the Targaryen's underneath his hammer and wipe them from the history books like Tywin Lannister wiped out House Reyne. As for Visenya, the last thing of his Lyanna. He will keep her so Lyanna will always be close to him. He wouldn't remove the last thing of her from this world or him. Eddard his brother would agree.
As for Rhaegar, he was heartbroken over the death of his second wife. He was so warped with prophecies; he lost the true purpose of everything. His mad father was still in power, Lyanna's dead, Visenya is in his mad fathers clutches to suffer like his mother had, Elia was giving him the cold shoulder due to his betrayal and actions, and the seven kingdoms new peace is surviving by a thread. It hurt even more as Visenya looked just like her mother. It was hard to look and get attached to her. He had to stay away. Looking at her was looking at his failure.
Elia knew about the marriage Rhaegar wanted to have with Lyanna and consented to it but she never agreed for things to happen like this. He was to talk to the North and explain things about everything, to include removing his father from the throne. But instead, he got impatient and jumped moved ahead. He risked the lives of her, their kids, Lyanna, and Lyanna newborn. In result the realm was torn, the lovely Lyanna is dead, and the King is still around to torture them still. She doesn't know if she could forgive him for all of this.