In a series full of subterfuge, where everyone is plotting something, one devious spymaster reigns supreme: Varys the Spider. He's the guy behind the guy at any given time, the one pulling the strings that control the Seven Kingdoms. And in the HBO show Game of Thrones... he doesn't really have anything left to do. Yes, technically he's working for Dany or something, but he's not... really... doing all that much right now. He's just part of her entourage, standing around looking vaguely worried with Tyrion while she runs about setting armies on fire.
TV show Varys repeatedly says that he's working "for the realm," and he's going to do whatever necessary to save the people of Westeros.
But book Varys? Book Varys is running another game entirely.
In A Song of Ice and Fire, Varys is still a bald eunuch from Essos, and the Master of Whispers for Westeros. He's also trying to bring the Targaryen dynasty back to King's Landing. But Dany is not the Targaryen he's rooting for. Last we saw Varys, he was murdering Kevan Lannister to pave the way for Aegon Targaryen to swoop in and take the Iron Throne.
And that might not be the only thing he's up to.
Remember that dude Illyrio, who gave Dany her dragon eggs? In the books, he's also BFF's with Varys from way back in the day. Apparently, young Varys was born a slave in Lys, where he hung around with a troupe of mummers (essentially actors) and learned the art of disguise. He was then bought from the mummers by a creepy wizard man, who castrated Varys as part of a blood magic ritual and left him to die.
Varys did not die, though. Instead, he became a master thief in the city of Myr, before being chased to Pentos, where he met a poor sell-sword named Illyrio. They cooked up a grift together: Varys would steal from people, and Illyrio would offer his paid services to get their lost possessions back. Together, they expanded their "business" into a network of spies who could "steal" and "retrieve" valuable information for their clients.
Varys eventually became so well-known as a spymaster, that Dany's daddy brought him to Westeros to spy for the Iron Throne. On the surface, Varys has been working for the Targaryens ever since. According to him, he even saved lil' baby Aegon Targaryen from being murdered by the Mountain during Robert's Rebellion. Varys claims that he switched out the royal baby for a peasant baby, and spirited the little prince across the sea to Essos. This baby apparently grew up to be the Aegon Targaryen who's now trying to invade Westeros with the help of Illyrio and the Golden Company.
Tyrion meets both Illyrio and cool teen Aegon on his trip east, and they tell him the same story about Aegon being saved as a baby, and raised to take back his daddy's kingdom. It seems almost... believable.
So, if Varys is telling the truth about all of this, then he's still a Targaryen loyalist who's working for the exiled prince.
...but since when has Varys ever told the truth?
After all, Illyrio and Varys are used to working together to get what they want.
It seems a little strange, after all, that Illyrio would have a secret Targaryen kid up his sleeve and not reveal him to Dany and her brother. Or that he would give his three priceless dragon eggs away, without saving even one for the wee prince Aegon. Or that his dead wife looked so much like a Targaryen, and that his house is full of clothes for a little boy, even though he is apparently childless.
Get ready to put on your tin foil hat, because a lot of fans think that "Aegon" is not a true-born Targaryen at all, but Illyrio's son with a Blackfyre woman. (The Blackfyres were a "bastard" branch of House Targaryen, who fled to Essos and founded the Golden Company far in the distant backstory. Don't worry about it.) The male line of the Blakcfyres has died out... but the female line could have survived. Illyrio's dead wife could have been one of them. And some fans even think that Varys could be one, too.
He does shave his head, after all, and we all know that those Targaryens love to hide their shiny, silvery hair. He was also castrated in a blood magic ritual, and if Melisandre has taught us anything, it's that king's blood has some pretty wacked out magic. Blackfyres might be bastards, but they still have king's blood. And it's always possible that Varys wasn't made into a eunuch just for fun, but to prevent him from fathering any more Blackfyres.
So we know that Varys is working with Illyrio to set up Aegon as the new king. But is Varys really working for the Targaryens? Or is Aegon just Illyrio's platinum blond son? Is Varys working for Illyrio, for old time's sake? Or is Varys really a Blackfyre working for himself, to put his family on the throne at long last?
Or is that just what Varys wants us to think?
We don't know for sure. But if Varys is truly as devious as we've been told, it's safe to assume that his allegiances are not quite so simple.