I don't know much about the history of religion, but I found that part fascinating.
Certainly, there are many unanswered questions about 9/11 and much secrecy. "They" certainly have something to hide, even if it's just incompetence and embarrassment. I wouldn't be surprised if there's complicity at some level (NORAD's inability to get fighters in the air is particularly unbelievable). The Lusitania was certainly a deliberate provocation. FDR and others in Washington certainly knew more about Pearl Harbor than they told the naval and army commanders, Kimmel and Short (an excellent book: Day of Deceit by Robert Stinnett). The Tonkin Gulf incident was bogus. Whatever involvement or foreknowledge the government did or did not have, they certainly milked it for all it's worth (without morality, human beings are simply pragmatic opportunists with mythology as justification).
The movie referred to "Criminal elements within the US Government... " The point is that coercive Government is crime. By natural law, any aggression against person or property is criminal, and "the State is a vast engine of institutionalized crime and aggression, the 'organization of the political means' to wealth" according to Murray Rothbard (The Ethics of Liberty).
There have been major players behind the scenes, or, sometimes right out in the open, like the Morgan and Rockefeller interests. Rothbard goes into great detail about this in A History of Money and Banking in the United States. You can also get some free stuff on the web from mises.org:
Our current housing boom/bust (and all other system-wide booms and busts) is the result of the fraud of fractional reserve banking and the crime of counterfeiting (by the Fed). This criminal fraud transfers income to certain elements of the financial elite and those who are favored by them, including the military-industrial-congressional-media-university complex. I wouldn't be surprised if we're moving toward a world currency controlled by a world government which can turn off anyone's RFID chip when he misbehaves (the ultimate perpetual parent!). Of course, we already had a universal currency controlled by individuals over 100 years ago: Gold. Oh well.
Near the end of the film, the narrator mentioned a new consciousness: "Earth as a single organism." This sounds too much like environmentalist religion. I say that the human being is a single type of organism with a certain universal nature which does not have to be divided into different religions or other artificial or delusional categories (another point made by the film, and, of course, by Stefan Molyneux). There is a science of human nature, of human action, and of human society, and I think Rothbard, Rand, and Mises came very close to the truth in many areas. Any thinker who begins with the evidence of the senses, logic, rationality, and the irrefutable self-ownership of each individual human being should be able to work toward the truth. And the antidote to Leviathan (and domination in general), of course, is to speak the truth without irrational fear.