The United States had multiple opportunities in the 1990s to go against al Qaeda. At one point, as we all remember, Sudan wanted to hand him over to the US but we said "no".

The United States was not concerned, primarily, with terrorism. International organizations like al Qaeda were significant enough to discuss, but certainly not to actually attack. When Bush got his first national security briefing, he was told that the threats to the US were, in order of danger: (1) China, (2) Iran and North Korea nuclear programs and (3) al Qaeda. Of these threats, al Qaeda was the most ephemeral - no organization can maintain the level of excitement and fervor to sustain long-term activities of this nature.

Looking at previous statements and incidents (like the spy plane the Chinese forced down) it is clear that the Bush administration was looking elsewhere. The war on terror strained a lot of relationships that had no problems. The old maxim of "if it isn't broken, don't fix it" comes into play. Why would the US want to expend so much political, economic and human capital tracking down a group of terrorists? Bush himself even alluded to this in his "million dollar missile into a ten dollar tent" statement.

9/11 also did a lot of damage to the US economy. Why would a President or anyone else in the government intentionally sabotage their means of making money?

Iraq certainly became a target of opportunity immediately after 9/11, and that fed into the US concern about Iran (I am certain the idea was to have bases in Iraq in the long term). However, conspiracies are very difficult to maintain. People talk. Look at wikileaks. Look at the Pentagon Papers.

If I had ever heard anything that made any logical sense, I would have at least given that version of events credit as "plausible".