After so many betrayals and deaths of our favorite characters, while the worst people in Westeros have lived to fight another day, all the bad stuff has to be over, right? No more of the good guys are going to suffer. Everything's going to work out for everyone going forward. Right? Of course not! This is Game of Thrones. No one is safe. And one of the worst things is still to come: Varys will betray Daenerys.
Varys's plan on Game of Thrones is, and always has been, a spiderweb. But, as Varys himself has made clear, his endgame is to put someone on the throne who will prioritize the needs of the common people of the Seven Kingdoms. While Dany has appeared to be the queen of the people in the past, her behavior has become much more brutal as of late, and Varys has begun to question the kind of ruler she'll be. And that's bad news for Daenerys, because it means Varys will double-cross Daenerys.
Varys's Loyalty Is To The Citizens, Not To Daenerys
Varys has said all along that his allegiance is to the lowborn, the common people. He's even told Dany as much in Season 7's second episode, when she questions his loyalty:
"You wish to know where my true loyalties lie? Not with any king or queen, but with the people. The people who suffer under despots and prosper under just rule. The people whose hearts you aim to win. If you demand blind allegiance, I respect your wishes. Grey Worm can behead me or your dragons can devour me. But if you let me live, I will serve you well. I will dedicate myself to seeing you on the Iron Throne because I choose you. Because I know the people have no better chance than you."
He will be loyal to Daenerys as long as she prioritizes the well-being of all her future subjects—but only under that condition.
Daenerys Is Starting To Act Like Her Father
Season 7 was full of reminders that, like her Mad father, Daenerys can be quite impulsive. At times, it seems she has lost sight of her goal to be a queen for the people. Most of all, she simply wants to be queen.
This has been illuminated in her arguments with Tyrion and Varys, and especially in the instance in which she executed the Tarlys when they refused to pledge their loyalty.
Varys Hates Both Magic And Royalty, But Daenerys Is A Magic Queen
Varys has made plain his feelings about royalty. He laments that has yet to see a just ruler, and he distrusts Daenerys will be much different from her father.Ever since he was castrated by a sorcerer as a child, Varys has hated magic. He even detests all those who use it. Well, dragons are the biological manifestation of magic. Those are two strikes against Dany.
Varys Doesn't Want Another Mad King (Or Queen)
After the dragons burned the Tarlys, Tyrion and Varys drank away the horror of the event in the throne room of Dragonstone. Varys recalled the times he watched the Mad King do virtually the same thing, all the while telling himself he was not the one doing it, trying to shirk his complicity. It's clear he does not want to go through that again, and Daenerys's behavior makes him uneasy.