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.
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. What's left of her is buried in the crypts right down there.”
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.
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.
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.
But Jon Snow, who is actually Aegon Targaryen, does have the best claim to the Iron Throne, according to the “rules.” His actual father, Rhaegar, was Daenerys' older brother. So Jon is the grandson of the Mad King and in the direct line of succession — Rhaegar's siblings are secondary to his children.
But, while time may heal all wounds, 10 years certainly wasn't enough time for Alicent's wounds to heal over being lied to by Rhaenyra. We last saw her find out the truth in "We Light the Way" that Rhaenyra lost her virginity to Ser Criston Cole (Fabien Frankel).
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.
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.
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 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 her victory, she became known as 'The Black', or 'The Black Queen', both for the name of her faction, and for her wrath towards those that had opposed her. All modern Targaryens can trace heritage to Rhaenyra, through either her son Aegon or her son Viserys.
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.
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 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.
“The Princess and the Queen” opens up with Rhaenyra giving birth to her third child, another boy. Laenor decides they'll name him Joffrey after his late lover who Criston beat to death right before he and Rhaenyra wed.
That's right, during the Oct. 2 episode of House of the Dragon, Rhaenyra (Emma D'Arcy) and Daemon (Matt Smith) stopped fighting their feelings for one another and finally got together. However, this was more than just an illicit liaison, as Rhaenyra and Daemon got married at the end of the episode.
Martin's Fire & Blood book are accurate, then Daemon will cheat on Rhaenyra with two significant characters in House of the Dragon.
Daemon seduces Rhaenyra in such a way to cast aspersions on her virtue so that Viserys has no choice but to let him wed his niece, Targaryen style.
It isn't explicitly stated in the show, but because we learn after episode six that all three boys have dark brown hair — and despite Rhaenyra and Laenor's matching blond color — it has been strongly implied that they are actually the children of Ser Harwin Strong, the Lord Commander of the City Watch.
George R. R. Martin's Fire And Blood shows Rhaenyra Targaryen's vengeful side and as a result, she has committed some despicable acts. Rhaenyra Targaryen is one of the principal protagonists of House of the Dragon. She's the heir of King Viserys I Targaryen, despite the tradition of sons taking the throne.
With Valerie Targaryen who is still adjusting to finding out she is the twin sister to Jon Snow as well as the secret daughter of Rhaegar Targaryen and Lyanna Stark. At the Dragonpit where the meeting of the most powerful people in Westeros gathers to meet.
At the end of Thrones, Jon—who's discovered he's a Targaryen and reluctantly killed his hookup partner/aunt Dany—has been banished to the Night's Watch by his biological cousin/adoptive half-brother Bran, the new king of the Six Kingdoms.
In other words, Jon's claim would be stronger than Daenerys' not primarily because of his gender but because his father, Rhaegar Targaryen, was the heir to King Aerys II Targaryen; Jon is the heir of the heir. Daenerys, meanwhile, though she is the only surviving child of the King, is Rhaegar's younger sibling.