In the books, during her reportedly unfulfilling marriage to Laenor, Rhaenyra is rumored to have taken Ser Harwin Strong as a long-term lover. Given that she's married, their relationship is certainly forbidden, but it reportedly lasts for several years.
By the time we reach episode six — which occurs more than 10 years later in the show's timeline — Harwin was revealed to be Rhaenyra's primary lover and the father to her three children.
Otto Hightower had informed the King of Daemon and Rhaenyra's "coupling," as he nervously called it, even though she actually slept with Ser Criston Cole.
King Viserys was so angered that he ordered both factions separated, Alicent's to King's Landing and Rhaenyra's to Dragonstone - and to put an end to any more salacious rumors, Viserys commanded that Harwin Strong leave Rhaenyra's service and return to his family's seat at Harrenhal.
After nearly seeing the two have sex in a brothel in Episode 4 and seeing their crackling chemistry in Episode 5, the fateful moment of Rhaenyra having sex with Daemon was both shorter than expected and literally too dark to see.
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).
After her lustful time with Criston Cole ended, and her marriage to Laenor Velaryon began, the new couple, future Queen and King consort of Westeros agreed to sleep with whomever they want, for it best suited them to be happy. Rhaenyra chose to sleep with Harwin Strong, and the affair brought them 3 children.
Rhaenyra will have two marriages (and two lovers) in House of the Dragon, with six children (technically three by each husband, the suspicion that the first three are by another man is a source of much violence and discord in Westeros).
The rumored lover of Princess Rhaenyra Targaryen, Harwin is believed by some to have been the real father of her three sons with her first husband Ser Laenor Velaryon, (Jacaerys, Lucerys, and Joffrey).
8 Rhaenyra Loves Her Uncle
In Fire & Blood, however, Rhaenyra is in love with Daemon from a young age. Things change after she meets Criston Cole. Nevertheless, George R. R. Martin's books show that Rhaenyra's first love was Daemon, whereas House of the Dragon has a slower build-up between the two.
Also, he may have realized the gravity of the situation (he was about to become very intimate with his niece in a brothel) and felt some sort of guilt and shame. These things mixed together, making Daemon physically and emotionally unable to complete what he set out to do.
In House of the Dragon episode 8, Rhaenyra Targaryen is pregnant with her daughter Visenya. Despite Rhaenyra and Daemon's excitement over having another child, their daughter will tragically never take a breath of air.
Yes they did actually love each other. He definitely loved Rhaenyra that much is clear and I honestly believe he loved her until the end (his death). He wasn't faithful but he did love her more than any other woman he has ever been with.
So, who is the real father of Rhaenyra's children? In the show and in George R.R. Martin's Fire and Blood novel, it is heavily implied that Ser Harwin Strong, a knight and the captain of the City's Watch, is the true father of Jacaerys, Lucerys, and Joffrey.
Back in her chambers, Rhaenyra's gaze lands on the handsome Ser Criston Cole (Fabien Frankel). After some initial reluctance by Criston, who has much more on the line as a lowborn member of the Kingsguard, Rhaenyra playfully seduces her long-standing crush and they have sex.
Now that he is gone, Rhaenyra will be in pain, mourning the loss of the only true romantic love in her life while dealing with children who may lash out without a proper father figure.
Jacaerys, Rhaenyra's eldest son, and his two younger brothers have spent their short lives surrounded by whispers that their real father was Ser Harwin Strong. It's an open secret that these “strong” boys aren't the sons of Laenor Velaryon.
Rhaenyra's second son with Prince Daemon would also later rule as King Viserys II Targaryen, as both sons of his brother Aegon III, Daeron I and Baelor I, later died without issue.
In Fire & Blood, the book House of the Dragon is based on, Daemon and Rhaenyra go on to have two boys: Aegon and Viserys. Yup, another Aegon and another Viserys.
It was abundantly clear in the season finale that Daemon truly values Rhaenyra as the queen, and it doesn't appear to be for his own gain. All of his actions indicate that he looks to her as his leader even before she's taken power and has every intention to get her to her rightful throne.
The story of the princess and her valiant knight did not end as a fairy tale, though. A sordid and controversial story began to spread that Rhaenyra lost her virginity to her uncle Daemon at age 16. No one knows if that is true. But Targaryens had long married within the family to keep their bloodlines pure.
— then Rhaenyra officially loses her virginity to Ser Criston Cole.
Ser Criston Cole, we have to understand, was never a good guy. He wasn't an honorable knight who went over to the dark side. He merely wore a chivalrous façade. He didn't want Rhaenyra to run away with him because he loved her despite his claims to marry “for love.” Nor was he heartbroken over her refusal.
Rhaenyra's Relationship With Criston Soiled His White Cloak
In "King of the Narrow Sea", Rhaenyra seduced Ser Criston after she herself was denied by her uncle Daemon (Matt Smith). She and her paramour spent the night together, and she was warm towards Ser Criston afterward.