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Whilst Rhaegar was plotting the removal of his father from power, Varys was trying to prevent Aerys from walking to the Great Sept or even trying to ask where his brother was, for Varys' little birds had informed him some days back of the grand council that Prince Rhaegar was holding in the Great Sept of Baelor to dispose of his father and for Varys it was essential that Aerys remain ignorant of what was actually going on under his nose until the very last moment. For although Prince Rhaegar may not have that much fondness for Varys, the Spider knew that in order for there to be peace in the Seven Kingdoms Prince Rhaegar had to become King Rhaegar, for despite his actions in starting the rebellion many of the small folk as well as the nobility still idolised Rhaegar and felt that he still had the potential to be the greatest king Westeros had ever seen. It helped Varys supposed that he had sent his little birds out into the streets to romanticise Rhaegar's absconding with Lyanna Stark and had had them paint it as a tragic love story, something that all could relate to. Though he had been careful to about sending his little birds to the north, for he knew that the northern lords still held a grudge against the Targaryen dynasty for the death of their liege lord's father and brother, and were not likely to forget that it was Rhaegar's actions that had led to their deaths. Though they had accepted through Lord Eddard Stark, to acknowledge Rhaegar as King simply because after the rebellion they held Lord Eddard in high esteem and would be willing to follow his lead.
Varys kept one eye on the door to the throne room waiting and anticipating for Prince Rhaegar to walk through the doors and announce the arrestment of his father, though as the minutes continued to pass by Varys began to worry that perhaps Rhaegar had been voted down by the Council of Lords and that perhaps after his actions in the rebellion they had voted to keep Aerys as King, something that would most definitely throw a spanner in all of Varys' plans. However, it appeared that Varys' fears were unfounded as the doors to the throne room flew open and in strode Prince Rhaegar flanked by two white cloaks Ser Arthur Dayne and Ser Oswell Whent, as well as the Commander of the City Watch Manly Stokeworth. Aerys surprise at seeing his son was written all over his face and became evident in the high pitched tone of his voice when he said "What is the meaning of this Rhaegar? Where have you been, why have you ignored all of my summons?"
Rhaegar stood in the middle of throne room drawn up to his full height and said in a voice of iron "I was in the Great Sept of Baelor father, praying for some strength and guidance for what I am about to say." Aerys snorted, his disdain for the Seven had become all the more apparent during the years since Duskendale. Rhaegar continued "I also met with the Lords Paramount except Lord Tully, who is still being held here. We discussed the future of our nation father, and in that future none of the Lords could see you in it either as King or otherwise. I believe and they agree with me that you have done enough during your reign to unbalance the realm, and your actions during the past year caused a rebellion to happen and to threaten the long worked for peace. I believe though it pains me to say it father, that you are no longer fit to neither rule the Seven Kingdoms nor call yourself King. And so it is with this in mind and with backing of six of the Seven Lords Paramount that I name myself King, and declare your crown and rule forfeit and hereby decree your arrest for threatening the peace of the Seven Kingdoms and declaring and acting on an impulse to have a Lord Paramount and his heir burnt to death."
There was a long silence in which Rhaegar's words sunk in and the two knights and Lord Stokeworth advanced toward the Iron Throne then Aerys as if snapping out of a trance began shouting "Traitors the whole lot of you! All of those Lords asking for more than they deserve, who are they to question the blood of the dragon? Hmmm, does not the whole world bow before the might of the Dragon?! I am the dragon not you Rhaegar, the day you were born was the day the dragon died! You who would accuse me of starting a rebellion with my actions! Did you not think before you took the Stark Bitch?! You took her and fucked her and got her with child oh yes you did! That grey eyed bastard is no Targaryen oh no he is not! You are no dragon nor are your children! I am the one true dragon, I AM!" And with that Aerys was led out of the throne room and toward the black cells by Lord Stokeworth and ten men from the Gold Cloaks, whilst Rhaegar stood on in the middle of the room watching with a sad look on his face.
Once Aerys' shouts had died down substantially, Varys saw Ser Arthur and Ser Oswell look to Rhaegar as if asking permission for something, when Rhaegar nodded his head Ser Oswell walked out of the throne room and Ser Arthur and Rhaegar advanced toward the Iron Throne. Varys watched fascinated by the way Rhaegar merely stood in front of the steps leading toward the Iron Throne for the longest time as if trying to assess whether or not it was the correct time to sit on his throne, yes Varys thought Rhaegar certainly would make a good king, perhaps even a great one. Eventually Rhaegar sighed and then walked up the steps and turned round and then, and only then did he look at Varys though he kept his face expressionless Varys could tell that the words he spoke pained him greatly "Lord Varys, you were witness to what happened here today. You saw the way my father raved and ranted about his rights and this right, you know that what has happened here today is for the best of Westeros correct?" Varys nodded, Rhaegar continued "Very well, tell your little birds to summon the Great Lords from the Sept of Baelor, and tell your man in the jails to release Lord Tully and to bring them all to the throne room." Varys nodded again and left to do as he was bid.
Once all the Lords Paramount and Rhaegar's wife and children were in the throne room Rhaegar beckoned Princess Elia, Princess Rhaenys, Prince Aegon and Prince Jon (the two princess were being carried by Princess Elia) up to stand beside him on the dais, Rhaegar spoke "Today my lords is a day that all shall remember, today is the day when a mad king was replaced by his son. I hope to serve Westeros and its people to the best of my ability for as long as I am able and I hope to work with you to maintain the peace in our land for as long as possible. My first order as King is to appoint Tywin Lannister as hand, Jon Arryn as Master of Laws, Mace Tyrell as Master of Ships, Lord Varys shall retain his position as Master of Whisperers, Grand Maester Pycelle will of course stay as Grand Maester, and Ser Gerold Hightower remains as Lord Commander of the Kingsguard and Master of Coin shall be Lord Stannis Baratheon. The coronation shall take place in four days time."
The next four days passed by in a whizz of activity, with there being lots to do to prepare and Varys spent much time going over the reports his little birds brought him, especially about how Lord Stark was still very much resentful of King Rhaegar and how he wished to take Prince Jon, (who Rhaegar had legitimised) back with him to Winterfell, and how Lord Eddard was struggling to truly come to terms with his sister's death. That was not all, soon after the coronation took place with the whole of King's Landing and the seven kingdoms in attendance, Tywin Lannister married his daughter Cersei off to Stannis Baratheon, something Varys was intrigued by and decided to keep an eye on for the time being. He hoped that now peace could reign in the seven kingdoms for he suspected that there would be more pressing threats in the future, and for them to be dealt with effectively the kingdoms would need to be united.