By the time of the House of the Dragon season 3 finale, almost everyone in Westeros has taken sides. The Blacks are for Rhaenyra Targaryen, the Greens for Aegon II. The rest of the realm is left to try and survive the chaos their conflict has caused. But Alys Rivers was never truly part of that system. She lives in the ruins of Harrenhal and seems to be ruled by a code of rules that is not at all connected with the political strife going on in Westeros at this time. She has met Daemon Targaryen, and Aemond Targaryen, and she’s had an effect on both men, in very different ways. She’s shown time and time again that she knows more than she is willing to share.
So whose side Is Alys Rivers really on? The simplest answer being that she’s not really aligned with either side. Alys doesn’t seem interested in sitting behind Rhaenyra or Aegon, nor does she seem concerned with helping either of them secure the Iron Throne for the sake of the crown. Her loyalty appears to be to something much older. The Old Gods, the magic of Harrenhal, the visions she has, and perhaps most of all, to her own survival. This makes her part of an elite minority in the Dance, as she is not actively playing the same game as the other players.
Alys is much older than she appears

Alys is described as a mysterious healer with a special connection to magic. Daemon and Aemond think she’s weird and maybe dangerous but they don’t seem to realize the extent of what’s going on. The story plays out to reveal that Alys’s history stretches far beyond what either Targaryen could have imagined.
Her connection to Harrenhal is tied to the ancient history of the castle. As a bastard born of House Strong, she survived generations of tragedy in its halls, eventually binding her to the ancient magic of the place and giving her a life span longer than was natural.
That history is fundamentally changing the lens through which her actions should be viewed. Alys is more than just another woman swept into the Targaryen civil war. She has seen enough history to know that this conflict is just another chapter in a much longer story.
And it explains why Alys is not that impressed by the power the Targaryens hold. Daemon and Aemond reach Harrenhal, thinking that their dragons, their titles, and their armies guarantee their freedom. But Alys has seen the mighty come and go for generations. She knows that kings and princes die, but the old power that clings to Harrenhal does not.
How Alys dealt with Daemon Targaryen

Daemon’s stay at Harrenhal is one of the most interesting examples of Alys behaving outside of normal politics. He takes the castle in Rhaenyra’s name, but Alys is no mere subject in his camp. Instead, she invades his mind and forces him to confront truths he’d rather not look at.
Alys’s potions, visions, and connection to the supernatural erode Daemon’s confidence. He is obliged to confront his guilt, his complex feelings for Rhaenyra and the repercussions of his life decisions. She not only advises him on military strategies, she also helps him realize that the war is only a small part of a much larger cosmic tapestry.
This is a prophecy, however, not a threat, and so her declaration that Daemon will die at Harrenhal is of great importance. Alys confesses that Daemon has a part to play in what happens next and instead of trying to shield him from it, she is encouraging him to go after it. Ultimately it is her influence that brings Daemon back to Rhaenyra and the destiny that awaits him at the God’s Eye.
Aemond believes he is in charge

Alys’ relationship with Aemond is very different but it shows us the same basic truth about her character. When Aemond takes Harrenhal, he appears to have all the power. He is a Targaryen prince, rides Vhagar, and believes his position grants him total power. But Alys is one of the very few people in his vicinity who is not afraid.
She becomes his confidant and lover. But their relationship is far more complicated than Aemond finding a sympathetic companion. Alys sees the deep insecurities behind his self-confidence, the rage that dictates his choices. She knows Aemond’s ambition makes him dangerous, but it makes him predictable as well. As he convinces himself that he is in control, the easier it is for Alys to predict his next move.
Aemond believes he is using Alys for his own purposes at Harrenhal but their conversations always suggest the opposite. Alys knows that Aemond is on a collision course with Daemon, and she’s quietly working to keep him on that course. Again, she is not the advocate of the Greens, but the director of one of their most visible figures into a fate she already knows.
Gayle Rankin on Alys’s True Allegiance

Actor Gayle Rankin has also said she doesn’t see Alys as a character that fits neatly on one side or the other of the show’s Black vs Green divide. Rankin has spoken about Alys’ uniqueness from the rest of the cast in interviews with Entertainment Weekly and Collider, particularly the unusual perspective she has on the realm due to her connection to ancient magic.
“Alys is a gateway to the older, stranger side of Westeros,” Rankin said, but also stressed her commitment to keeping the character grounded rather than turning her into a generic fantasy archetype. There has to be a balance; Alys behaves in deeply unsettling ways without being a typical villain. More interesting is the fact that she watches, in silence, the powerful self-destruct, aware that their political aspirations are short-lived.
Rankin also said that Alys is not interested in the traditional societal roles that women of Westeros are expected to fulfill. She doesn’t want titles, marriage, or a place at the royal court. She is in a different class to most of the characters caught in the Dance in that she has her own power and understanding of the world.
Alys Rivers: A Player, Not a Pawn

What Daemon and Aemond get wrong is that they think they have Alys under their command. When both men reach Harrenhal they are certain that their arrival signifies that they are the lords of the castle and its people. But instead Alys gently upends their assumptions. She is aware of the ancient forces at play beyond their political obsession, which neither man truly comprehends, and she needs no army nor dragon to change the course of events.
Which is why it is totally wrong to try to put Alys into either Team Black or Team Green. She is not meant for Rhaenyra or Aegon. She’s able to see the whole Targaryen struggle from afar. The royal family may think the fate of Westeros depends on who sits on the Iron Throne, but Alys knows kingdoms rise and fall, and the old powers of the world endure.
In the end, Alys Rivers is a master survivor, playing her own tune in the Dance of the Dragons, rather than taking part in it. She sways Daemon, she manipulates Aemond, she watches the Targaryens tear themselves apart, for a cause that predates either banner. One of the most compelling aspects of House of the Dragon is the question of whether that purpose is ultimately bound to fate, the Old Gods, her own survival, or something far stranger. But one thing’s absolutely clear: Alys Rivers isn’t anyone’s pawn.
