Just because she didn't write about this story .. doesn't mean she doesn't have any notes on the story
I know, but we don't know what direction she was headed. Had she published we would have known what line of investigation she took. That in turn could lead to clues about who she is protecting.
I think that Fitzgerald is going after illegal State Department (or CIA) leaks. Miller tipped off a terror mosque to an impending federal raid and ruined one of Fitzgerald's other investigations. He wants to know how Miller got her info, and maybe he believes that the sources for the Plame info and the terror mosque info are one and the same.