In Fire and Blood by George R.R. Martin, Rhaenyra does indeed take the Iron Throne and become queen over the Seven Kingdoms, however, her reign is short-lived.
Rhaenyra Targaryen Takes the Iron Throne, but Only For a Moment. While the Green forces were away from King's Landing, they foolishly left the capital sparsely protected. That allowed Rhaenyra and Daemon to easily take the city, where she sat on the Iron Throne for half-a-year.
Joffrey Baratheon spoils Rhaenyra Targaryen's fate on Game of Thrones. As Joffrey tells us, eventually, Rhaenyra's half-brother Aegon Targaryen will feed her to his dragon Sunfyre. She dies as her son, Aegon III, watches.
King Viserys dies at age 52, having reigned over Westeros for 26 years. Princess Rhaenyra rules as Queen Rhaenyra for about half a year on the Iron Throne. As many of her children are killed, she flees King's Landing after a riot known as the Storming of the Dragonpit, and is eventually caught.
The simple answer is that after Rhaenyra was deposed and murdered by the greens, her half brother King Aegon II commanded that her name be redacted from the history books, and that she never be considered a true queen.
After teasing their deep connection for weeks, making out in a brothel, and flirting their way through King's Landing, uncle and niece at long last did the dirty. Not only that, but Rhaenyra and Damon literally had sex on the beach.
The moment happens in season 3, episode 4, “And Now His Watch Is Ended,” when Joffrey Lannister is chilling with Margaery Tyrell and giddily explains, “Rhaenyra Targaryen was murdered by her brother, or rather, his dragon. It ate her while her son watched.
Rhaenyra's eleven year-old son, Aegon the Younger, was crowned king, and married to Aegon II's daughter and only remaining child, Jaehaera Targaryen, uniting the claims.
The new king, Aegon, is the son of Viserys and Alicent Hightower, his second wife. Rhaenyra's gender has led to wide disputes concerning her claim to the throne, and many in the Seven Kingdoms believe Aegon, as the firstborn male has more claim than her.
The shock of the loss of her father, combined with the Greens' ruthless betrayal sends her into early labor. Without modern medicine, a baby born so early had very little chance of survival in the best of circumstances - and in these terrible conditions the baby, a girl named Visenya, is stillborn.
During their walk, Joffrey stops at one point to show her the final resting place of Rhaenyra Targaryen, who's now long dead. "Rhaenyra Targaryen was murdered by her brother, or rather his dragon," says Joffrey. "It ate her while her son watched. What's left of her is buried in the crypts right down there."
Rhaenyra and Daemon's Marriage
Soon after being widowed, Daemon and Rhaenyra marry each other in secret when he is 39 years old, and she is 23. Their marriage causes a huge scandal at court and another rift between Daemon and Viserys, but it is eventually accepted.
With both Rhaenyra and Aegon gone, there's one clear person to inherit the throne: Rhaenyra's son Aegon, known as "Aegon the younger" in the books (her older sons had all died by this point).
The Dance of Dragons
Rhaenyra, furious over the injustice, proclaimed herself the Queen of the Seven Kingdoms. This proclamation sparked the entire realm to go to war.
Alas, the baby did not survive and while it wasn't shown very well on camera, there were debates among fans whether the baby was normal-looking or deformed.
Daemon made many enemies from Lys, Myr, and Tyrosh, and he slew Craghas Drahar in 108 AC. After conquering all but two of the islands, Daemon declared himself King of the Stepstones and the Narrow Sea in 109 AC, being crowned by Corlys the Sea Snake.
Nonetheless, Rhaenyra and Daemon's youngest son becomes King Viserys II Targaryen, with the crown passing through his line. New episodes of House of the Dragon release Sundays on HBO/HBO Max.
Is Daenerys Targaryen related to Rhaenyra? Daenerys Targaryen from Game of Thrones is a distant descendent of Rhaenyra Targaryen, who she has been compared to in House of the Dragon.
Daemon strangled Rhaenyra because he felt betrayed by Viserys. “It's a moment that I think is surprising and shocking for Daemon as a character, but I also think it's one of those things that's been set up over the course of the entire season.
Rhaenrya takes the news of her son's death none too well. The look she gives the camera upon Daemon delivering the news suggests she is ready to burn Alicent's family alive. The Season 1 finale was named “The Black Queen,” and it seems that Rhaenyra is finally ready to take on that title.
Though Rhaenyra has sympathetic motives, having been declared her father's heir, her treatment of the dragonseeds and Velaryons, along with her tyranny means she is regarded as a villain.
According to the accounts of Septon Eustace, prior to her turning sixteen, Rhaenyra lost her virginity to her uncle, Prince Daemon, after he seduced her.
The relationship between the two started in earnest in episode five, after Criston slept with Rhaenyra (played then by Milly Alcock). Alicent speaks to him to see if he knows anything about Rhaenyra sleeping with her uncle, Daemon (Matt Smith), but Criston confesses to their own liaison instead.
Everyone who was a teenager in House of the Dragon Episode 5 has now been recast in Episode 6. Rhaenyra, Alicent, Laenor, and Laena are all being played by older actors to show they're all grown up now and ready for their own Game of Thrones.