Question: Maybe I'm just dumb, but when did Sydney find out that Vaughn was alive? I thought she didn't know. I'm so confused.

Answer: That makes two of us. I consulted with our resident Alias expert, Angel Cohn, about this, and here's her theory: "It seems like she probably has known all along. I'm guessing that the scene in the hospital when he was dying where they gave him some kind of pill and she said goodbye was all just a cover to make Prophet 5 think that he was dead."