One benign possibility is that the NSA was surveilling this agent for completely separate reasons. But Electronic Frontier Foundation's Kevin Bankston cautions that there "has been a greater level of cooperation since 9/11," so there's no reason to assume the NSA wasn't involved from the outset.
I asked FBI spokesman Richard Kolko if he'd describe, in generic terms, the level of interagency co-operation between the NSA and the FBI and the circumstances under which such co-operation would occur. Kolko said he was aware that my inquiry was pursuant to this still-emerging story and refused to comment. (At his behest, I've passed the inquiry along to the Department of Justice.)
A former FBI source who declined to speak on the record suggested that perhaps the NSA's involvement stems back to the origins of this controversy. As my colleague Zack Roth noted yesterday, in May 2005, former Defense Intelligence Agency analyst Larry Franklin was taken into custody by federal agents after a months-long investigation revealed he had handed over secret U.S. national security information to Israeli agents. That may be key, because, according to the source, for the most part, the NSA's investigative capability is limited to inquiries into their own people--and as a Defense Department agency, that would include Pentagon officials.
But, of course, the Harman conversation supposedly took place in October 2005, several months after Franklin had already been indicted, and around the same time as Franklin pleaded guilty. And that raises the question: if the NSA was involved because of Franklin (still a big if), why were they still involved after his specific case was all but wrapped up?
I'll pass along any more information as I learn it--the explanation may prove interesting.