Sounds to me like he's still perpetrating a cover-up:
Nichols' sojourn in the Muslim region of the Philippines, and the strong resemblence between the police sketch of John Doe Number Two and Jose Padilla, both point not to some nefarious government plot, but to an Al Qaeda connection.
The Philippines are listed as 5% Muslim, although some areas are much higher proportion. I have never seen anything about him spending time in the specifically Muslim parts of the Philippines.