Sofie

She fought her true nature and in the end lost. There were signs of her darkness before. It was a brilliant twist having her go over the the dark side. In their world darkness begets light but the end comes when the darkness begets darkness. There was reason why her shifting sides makes sense. The trinity explosion was the end of magic and the beginning of science overcoming magic. A brilliant series I just wish it would have played out until the end. Worst mistake HBO ever made cancelling it!

We don't really know - it seems that she is both.

In the recent interview Daniel says the following that will give us some closure. I was very happy to read his interview after all these years!

AVC: What were your plans for what would have come in the four unmade seasons?

DK: Like I said, I’m not going to claim I knew the minute detail. Season three is five years later. We find Jonesy—he survived his gunshot wound and is pitching for a professional baseball team. His wife [Libby] is a typical baseball wife back in ’39. The carnival is completely split up; everybody’s gone their separate ways. The only vestige of the carnival as it was is Ben and Samson, and they’re working at another carnival, still on Management’s trail.
Then on the Brother Justin side, we find he’s become this incredibly politically influential radio preacher. And there’s Iris and Sofie, and they’re both in this fight. He’s a shell, almost, and these two women are in a power struggle over who’s controlling Brother Justin. Sofie is Brother Justin’s wife. Of course, she’s his daughter, but he doesn’t know that. She knows that. She could bring him down pretty easily, but she’s afraid of herself now, too.
Then we introduce, in the very first episode, you see this 4-year-old kid come running up and hugging Brother Justin, saying “Daddy.” Is this Brother Justin’s child, or is this Ben’s child, because they both had relations with Sofie? That would kind of tee us off to the second one. That would take us through the war. And then the first half of that would be, “Avengers assemble,” winds of war calling them together, gotta get this group back together again. Ben’s like, “This isn’t just about me. This is about us.” And pulling everybody out of their lives and answering this call, and moving into going to Europe to try to acquire these documents or… I knew they were going to be talismans. What they’re going to need when they’re engaged in this war. Then there’d be a confrontation of some sort at the end of season four.
Then taking us to the end, it’s all about the [atomic] bomb. It’s all about the Manhattan Project and worrying about it, finding out what it is. The Germans have a competing project, and trying to stop it. Trying to stop the bomb from happening, because in Ben’s mind, detonation of the atom bomb is the end of the world. What he doesn’t realize is that it’s just the end of his world. To him, it’s an end to Avatars; it’s an end to everything. But he’s misinterpreted it. He’s interpreted it as the end of the world. He thinks he’s saving the world, but what he learns before the end is that, “I have to let this happen, because if I don’t let this happen, mankind will remain in a state of adolescence.” He learns that’s really why Sofie is called the Omega. She is the only female, the last Avatar. What it’s all leading up to is two Avatars, she and Ben having this child. They actually have to sacrifice this child in the blast. That was my crazy notion.

"Seth Brundle: I've come here to say one magic word to you. Cheeseburger. "