While we wait to hear whether Patrick Fitzgerald indicts anyone in the Bush Administration, I think back to a conversation I had shortly before the 2002 elections with a friend who was in the White House Counsel's office. The friend said that having a Republican majority in the House and Senate mattered a great deal in the White House -- yes, it would help with legislation; but more to the point, the friend stated happily, "That means no investigations." As the friend noted, investigations had tripped up prior Presidents, but with the demise of the independent counsel statute, investigations would be controlled by Republicans -- and the White House had every reason to expect that it would be able to control them. (I had a somewhat similar conversation with another White House friend before the 2004 elections, but that is another story.)
But a funny thing happened to this plan: when Plame's outing as a CIA agent became an issue, Ashcroft recused himself (appropriately, given his close ties to some of the apparent targets), leaving the matter in the hands of his deputy, James Comey. Comey, in turn, appointed Patrick Fitzgerald, a Republican not known as a hard-core loyalist. The White House, angry that in this action as well as some of his hiring decisions Comey "erred too much on the side of neutrality and independence," made it clear that he would not be appointed Attorney General. (Indeed, a White House official gave an additional quote that Orin higlighted at the time, and that I still find disturbing in describing the leadership of the Department of Justice: "The objective in staffing is never to assemble the best possible team. It is to assemble the best possible team that supports the president." The whole Legal Times article is worth reading, although you need to subscribe to get access.)
Had Comey appointed someone who looked tough but in fact wouldn't really harm the White House, life would have been a lot easier in the West Wing. But Comey showed that darned independence, and now they may be in quite a pickle. (Of course, it could be that Fitzgerald issues no indictments and all this blows over. We'll just have to wait and see.)
I hope that the lesson the Bush Administration draws from all this is not that they made mistake in failing to appoint a more "loyal" Deputy Attorney General, but I wouldn't count on it.
A final note: the only other prosecutorial cloud on the horizon results from federalism. If the federal government controlled the units below it, there would be no indictment against Tom DeLay. When you control the levers of the federal government, state and local (like Comey's "neutrality") represents a wild card. The Bush Administration doesn't like wild cards (and in practice it often doesn't like federalism). But control right now seems to be in short supply.