Why does it have to be a DoD/CIA mission? It's quite possible it is Homeland Security gathering information on illegal immigrants, or possibly the FBI conducting surveillance.

I've seen these sorts of overflights regularly in the Baltimore/DC area. Most of the time it is Cessnas over a specific area (usually the FBI, judging from the shell company associated with the aircraft no.), but recently there was an umarked/blocked info aircraft canvasing Baltimore for a couple hours -- just the city, a very specific grid flight pattern. It was flying out of a commercial facility in Delaware.

My money is on surveillance targeted at locating illegal immigrants, using ELINT and photographic evidence together.