My guess is they're looking for something, even a component molecule or precursor, if not an actual agent or decomposition product.
The Constant Phoenix has whole air and particulate collection suites. Whole air isn't so great, because it uses engine bleed air, which itself is tapped off the 7th compressor stage in a P&W TF-33 engine. (HOT!)
The 13" filter papers, however, might gather something useful.
My guess is the White House Situation Room called the JCS, and directed a sortie with expectations they might get at least some kind of evidence.
They tasked us to fly after the shuttle re-entry accident, too. We found a lot of burnt stuff floating in the air.