Shortly after the second World Trade Center tower was hit, I burst in on Rice (then the president's national security adviser) and Cheney in the vice president's office and remember glimpsing horror on his face. Once in the bomb shelter, Cheney assembled his team while the crisis managers on the National Security Council staff coordinated the government response by video conference from the Situation Room. Many of us thought that we might not leave the White House alive. I remember the next day, too, when smoke still rose from the Pentagon as I sat in my office in the White House compound, a gas mask on my desk.
You have to wonder whether Clarke - an old associate of O'Neill, remember - would even WANT to suggest that it was all a false flag op (not that he would be allowed to publish that).
Seems to me like this article has been carefully crafted to just keep the pressure on Cheney et al. The comments are where the real action is at, especially because the big papers so seldom go anywhere near these stories.