What the hell is up with Tom Cruise movies?  Most of them are about where he uncovers a government conspiracy, then realizes he's not who he thinks he is, then restores his true identity.  And these are big budget productions.
I think the scientologists are funding these flicks as recruitment tools.  They stir up distrust in government, then they replace identities with alien worship or something.  I bet if you go back and watch these movies, there are some subtle references to scientology at the climax, where the hero wins.