Anvilicious (especially towards the end): General message - government secrets are bad.
Designated Hero: Paul is treated as the one we're supposed to sympathize with, even when his behavior is a near-textbook example of The Sociopath. It's taken Up to Eleven near the end when he's willing to threaten the lives of thousands of people to protect himself. Note that by this time, the media knows he has an atomic bomb, and it's just a matter of time before the lab is exposed; he chose to keep this whole thing going for no reason. It turns the Army into the Designated Villain. The movie clearly tries to paint Colonel Conroy as the bad guy, even though every single action he takes is justifiable, given what Paul has pulled.