"Rhaegar fought valiantly,
Rhaegar fought nobly.
And Rhaegar died."
―Jorah Mormont

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Prince Rhaegar Targaryen was the eldest son and heir to King Aerys II Targaryen, holding the title of Prince of Dragonstone. He was the older brother of Viserys and Daenerys Targaryen and husband of Elia Martell, with whom he had two children: Rhaenys and Aegon Targaryen. Secretly, however, his marriage to Elia had been annulled and he remarried to Lyanna Stark. Together, the two secretly had a son: Jon Snow, who was raised by Lyanna's brother Eddard Stark as his bastard son to protect the child from those that sought the destruction of House Targaryen after Robert's Rebellion.

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Rhaegar was said to have ignited the rebellion after allegedly abducting Lyanna Stark. Lyanna's betrothed, Lord Robert Baratheon, slew Rhaegar at the climactic Battle of the Trident.

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Background
Prince Rhaegar Targaryen was the eldest son and heir to the Mad King, Aerys II Targaryen, by his sister/wife Queen Rhaella Targaryen. Tywin Lannister, who served as Aerys's faithful Hand of the King for nearly twenty years, desired that he would agree to a marriage between Rhaegar and his own daughter Cersei. Young Cersei herself hoped that she would marry Rhaegar some day. King Aerys denied the request, however, and insulted Tywin by indicating that such a match would be beneath Rhaegar.

Instead, Rhaegar was married to his distant cousin Princess Elia Martell of Dorne, with whom he had a daughter named Rhaenys and then a son named Aegon.

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During the great Tourney of Harrenhal, where all the prominent lords of Westeros assembled, Rhaegar faced off against Ser Barristan Selmy in the final tilt and won. Instead of giving the victor's wreath to his own wife Elia, however, the entire crowd of hundreds of people fell silent as he rode past her and gave it to Lyanna Stark of Winterfell, to name her as the tournament's Queen of Love and Beauty. This was doubly controversial, as Lyanna was herself already betrothed to marry Robert Baratheon. Some months later, under as-yet unknown circumstances, Rhaegar and Lyanna run away secretly in order to get married.

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Lyanna's oldest brother Brandon then rode to King's Landing to demand the return of his sister, but King Aerys imprisoned him. When their father Rickard went south to demand his son's release, he was imprisoned as well. The Mad King then brutally executed both of them by burning Lord Rickard alive with wildfire in front of the Iron Throne and baiting Brandon to strangle himself to death. In response, Eddard Stark and Lyanna's betrothed, Robert Baratheon, joined forces with several other houses to overthrow the Targaryen dynasty. This war became known as the War of the Usurper or Robert's Rebellion. After initially remaining away from the fighting in Dorne, Rhaegar was summoned to lead the Royalist forces in what would be the climactic confrontation of the war, the Battle of the Trident.

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The rebel army continued on to King's Landing - but Tywin Lannister's army arrived there first. Feigning that he had come to help Aerys, Tywin really saw that with Rhaegar dead the Targaryen cause was lost, and was there to betray him to gain favor with the rebels after the war ended. After being let inside the gates, Tywin's army promptly began to brutally sack the entire city. Rhaegar's father the Mad King was himself killed by his own Kingsguard, Tywin's son Jaime Lannister (to stop him from enacting the Wildfire plot to burn down the city). Meanwhile, Lannister soldiers gained entry into the Red Keep. Ser Gregor Clegane, known as "the Mountain that Rides", cornered Rhaegar's wife and two small children in the royal apartments. Gregor killed Rhaenys and baby Aegon while their mother Elia watched helplessly, then raped Elia, before killing her too.

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Shortly before the sack, however, Rhaegar's heavily pregnant mother Queen Rhaella had been sent to safety on Dragonstone island, along with his younger brother Viserys. Not long after they arrived, however, Rhaella died giving birth to Rhaegar's younger sister, Daenerys Targaryen. Viserys and his newborn sister then fled into exile in the Free Cities, across the Narrow Sea, before Robert's soldiers could arrive on the island.

Lyanna Stark did not survive much longer: after arriving at King's Landing in the aftermath of the sack, her brother Eddard rode south with his companions searching for her, before finding her at the Tower of Joy in the western mountains of Dorne, protected by the last of the Targaryen Kingsguard under the legendary Ser Arthur Dayne, who had been ordered to keep her safe by Rhaegar himself. Eddard and his companions fought them in an epic confrontation, at the end of which all were dead except for himself and the wounded Howland Reed.

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Eddard raced inside only to find that Lyanna was dying from childbirth to Rhaegar's last child and heir. Lyanna made Eddard promise to keep him safe because if Robert ever found out that Rhaegar had a surviving son, he would kill him. Eddard departed with Rhaegar and Lyanna's newborn son and took him back to Winterfell, where he passed him off as his own bastard son fathered on the campaign: Jon Snow.

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Barristan Selmy: "Viserys never told you?"
Daenerys Targaryen: "He told me Rhaegar was good at killing people."
Barristan Selmy: "Rhaegar never liked killing. He loved singing."
— Ser Barristan recounts his time with Rhaegar.

Before his alleged abduction of Lyanna Stark, Prince Rhaegar Targaryen is said to have been a very popular figure in the Seven Kingdoms in contrast to his erratic father, King Aerys. Despite the superb skills he displayed while participating in the Great Tourney at Harrenhal, where he mysteriously crowned Lyanna as the Queen of Love and Beauty instead of his own wife Elia Martell. Ser Barristan Selmy (whom Rhaegar had unhorsed in the final joust) described Rhaegar as a peaceful man who much preferred singing over fighting and killing.

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Rhaegar was a highly intelligent person who loved to read, so much that he was late in his decision to take up swordsmanship. He was an extremely charismatic man, shown by the fact that those who followed him were loyal to him and some believed him to be the finest man they ever met. However, this loyalty would come at a cost to some people, including Rhaegar himself. For example, Ser Arthur Dayne and Ser Gerold Hightower did not accompany Rhaegar at the Battle of the Trident because Rhaegar had ordered them to stay at the Tower of Joy and guard Lyanna thus Rhaegar had ultimately doomed them to die at the hands of Lyanna's brother, Eddard.

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Although Rhaegar proved to have been admirable enough that a great many men followed him to defeat at the Trident because they believed in him and his cause, there were those, mainly Robert Baratheon, who viewed Rhaegar as an evil man. This is probably a biased opinion since Robert was plunged into depression by the loss of the woman he claimed to love, and the common theory that Rhaegar abducted her made him a cruel man in Robert's mind. Oberyn Martell also had an unfavorable view of Rhaegar for running off with Lyanna and leaving his sister, Elia. Also, Viserys Targaryen, Rhaegar's younger brother, thought that Rhaegar loved to kill people, derived from the basis that he was a great warrior, leading to Daenerys developing the same assumption. However, Daenerys would eventually hear a dramatically different account from Ser Barristan about Rhaegar.

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In my dreams, I kill him every night."
―Robert Baratheon shows his undying hatred of Rhaegar.

"Your brother Rhaegar was the last dragon."
―Jorah Mormont to Daenerys Targaryen

"When your brother Rhaegar led his army into battle at the Trident, men died for him because they believed in him, because they loved him. I fought beside the last dragon on that day, your Grace. I bled beside him."
―Ser Barristan Selmy to Daenerys

Daenerys Targaryen: "Did you know him well, Ser Barristan?"
Barristan Selmy: "I did, your Grace. Finest man I ever met."
Daenerys Targaryen: "I wish I had known him, but he was not the last dragon."
— Rhaegar Targaryen remembered.

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In the A Song of Ice and Fire novels, the tradition holds that the victor in a tournament may select any woman present and name her the queen of love and beauty, crowning her with a wreath of flowers and dedicating his victory to her.

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he victorious knight often chooses a woman he loves or intends to court, and it can be a source of scandal if the victor crowns a woman already bound to another man, or if a married man crowns someone other than his wife. Since both of these cases were true when Prince Rhaegar Targaryen crowned Lyanna Stark after winning a tourney at Harrenhal, it was particularly scandalous.

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Source:
https://jasmoonbutterfly.blogspot.co.uk/2017/08/rhaegar-targaryen-and-lyanna-stark-love.html