In '' Chain of Command , '' a book based on his groundbreaking New Yorker reporting , Seymour M. Hersh notes that an intelligence operation was set up at the Pentagon as a kind of alternative to the C.I.A . It was created , he writes , to find evidence of what Deputy Defense Secretary Paul Wolfowitz and his boss , Donald Rumsfeld already '' believed to be true -- that Saddam Hussein had close ties to Al Qaeda , and that Iraq had an enormous arsenal of chemical , biological , and possibly even nuclear weapons . ''