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. As a result, Rhaenyra has a lot of enemies and will end up fighting in the Dance of the Dragons in an attempt to press her claim.
So far, House of the Dragon has shown Rhaenyra to be compassionate, bold, and sympathetic. She's far from perfect but has plenty of positive traits. However, books like Fire and Blood go into much more depth regarding her actions later in life. She's far from a one-dimensional villain, but she does indulge in horrific behavior before the war's end.
10 Carrying Out A Purge In King's Landing
Rhaenyra Targaryen does manage to claim the Iron Throne before the end of the Dance of the Dragons. She rules for less than a year before fleeing back to Dragonstone. Her reign is initially welcomed and considered far better than that of her half-brother Aegon II. Before long, however, Rhaenyra indulges her vengeful side.
Rhaenyra initially forgives some of those who sided with Aegon. Notably, she spares former queen Alicent Hightower despite the enmity between the two. Then, Rhaenyra begins to kill those she sees as traitors. Her purge of King's Landing is bloody, fills the walls with heads upon spikes, and turns the peasants against her.
9 The Alleged Brothel Imprisonment
Fire and Blood, in-universe, draws from many sources to retell the Dance of the Dragons. None of these sources are fond of Rhaenyra, as they're either written by Aegon's allies or affected by Westerosi sexism. Many of them contain conflicting anecdotes that are designed to paint her in the worst light. As such, one of her worst acts may be a complete lie.
One source alleges that Rhaenyra took offense at Alicent describing her allegedly-Velaryon sons as bastards. In response, Rhaenyra has Alicent and her daughter Queen Helaena imprisoned in a brothel. She let anyone pay to assault them. It's a horrific act, but one that is dismissed as a falsehood by several other sources.
8 Condoning The Blood And Cheese Murders
Rhaenyra is far from the only vicious member of her faction. Daemon Targaryen, her uncle and husband, also does wicked things throughout the war. His most vicious act is the hiring of Blood and Cheese to murder a child. Following Lucerys Velaryon's death, Daemon pays the two assassins to exact revenge on Aegon's family.
Blood and Cheese capture Alicent, Helaena, and Helaena's three children. They force Helaena to choose which of her sons should die, but they kill the other. It's never said that Rhaenyra helped plan this horrific act, which lessens how much responsibility she bears. However, she never rebukes Daemon for it and shows no remorse or sympathy.
7 Harming Her Family With The Dance Of The Dragons
No member of the Targaryen family survives the Dance of the Dragons unscathed. However, Rhaenyra's five sons suffer more than others. Lucerys, Jaecerys, and Joffrey Velaryon all suffer horrific deaths, and her sons with Daemon survive with intense amounts of trauma.
The responsibility for their suffering lays primarily with Aegon's faction in the war. Alicent does try to keep them safe throughout the Dance of the Dragons. Nonetheless, the war and the decisions Rhaenyra makes cause her sons to suffer a great deal. However just her cause, Rhaenyra is willing to follow it through at great cost to all around her.
6 Declaring The Dragonseeds Traitors
During the Dance of the Dragons, Rhaenyra's faction finds itself with more dragons than riders. As such, they promise to reward anyone who can tame one. Several people complete this task. The most successful applicants are dragonseeds, bastards of House Targaryen and Velaryon.
The dragonseeds prove key to Rhaenyra's success. However, two dragonseeds, Hugh Hammer and Ulf the White, betray Rhaenyra at the First Battle of Tumbleton and inflict a great defeat. Rhaenyra declares them all traitors, even innocent loyalists, and orders their arrest or execution.
5 Potentially Having Helaena Targaryen Murdered
Helaena Targaryen's death is the breaking point for Rhaenyra's rule. Helaena was beloved by the smallfolk, so her death turns their dissent into outright fury. The circumstances around Helaena's death remain a mystery. Her body was found impaled on the spikes beneath her bedroom with no other evidence.
Popular belief is that Rhaenyra ordered Helaena's murder, despite being Helaena's half-sister. Most sources dispute this and instead suggest that Rhaenyra's actions traumatized Helaena. However Helaena's death happened, Rhaenyra likely bears some blame.
4 Ignoring The Smallfolk's Suffering And Throwing A Feast
Rhaenyra's rule of King's Landing is far from prosperous. The city suffers heavily from war and struggles further under Rhaenyra's harsh taxes. Its people starve and suffer and there's little aid available to them. Plenty of Rhaenyra's actions cause turmoil, but few more than throwing a lavish feast.
Rhaenyra celebrates her son becoming Prince of Dragonstone, which embitters the city's people against her. It's such a show of privilege that it does plenty to undermine Rhaenyra's rule. While it's not her worst act, feasting while her people starve is emblematic of nobles' disregard for commoners in Westeros.
3 Ordering Several Opposing Houses' Extermination
For all of her virtues, Rhaenyra suffers from a vengeful streak. She's quick to anger and slow to forgive, which isn't helped by the many slights and injustices throughout her life. Her conduct during the war attests to this. Rhaenyra shows she's willing to forgive some enemies, including members of Aegon's family, but is utterly ruthless toward others.
While in King's Landing, Rhaenyra chooses to go on the offensive. Rather than consolidate her victory and sue for peace, she pushes for revenge. In particular, she seeks to completely wipe out House Baratheon, Lannister, and Hightower. Although they are among Aegon's principal supporters, she suggests killing every member, including non-combatants and children. Although Daemon gives her the idea, Rhaenyra supports it wholeheartedly.
2 Trying To Have Nettles Murdered Because Of Gossip
When Rhaenyra turns on the dragonseeds, she tries to have most of them arrested and tries to murder one named Nettles. Nettles is an unusual dragonseed. She's potentially not of Valyrian descent and is the personal student of Daemon Targaryen. Their closeness causes several to speculate that they're having an affair, including Rhaenyra.
As such, Rhaenyra orders Nettles' death. Worse than that, she orders Manfryd Mooton to break the guest right and kill her in his own castle. In Westeros, such an act goes beyond murder and is widely considered one of the worst crimes a person can commit. Rhaenyra's willingness to violate sacred laws based on mere rumors is her worst trait.
1 Arresting Her Father-In-Law For Protecting His Family
Addam Velaryon is one of the most accomplished dragonseeds in the entire Dance of the Dragons. Even after he's accused of treason, he wins the Second Battle of Tumbleton for Rhaenyra's forces and dies a hero. When Rhaenyra orders his imprisonment, the only person on his side is Lord Corlys Velaryon.
The relationship between the two is unknown. Addam may have either been Corlys' son or his grandson. For daring to help his innocent relative, Corlys receives harsh punishment. Rhaenyra has her former father-in-law beaten and arrested and plans to execute him. For this, most of her allies desert her.