More on the plot from Newsweak...
http://www.msnbc.msn.com/id/13385543/site/newsweek/
The counter-terrorism officials also confirmed Suskind’s reporting that U.S. intelligence indicated that the subway attack was called off personally by Zawahiri. Though the officials said U.S. intelligence was still not certain why the attack had been cancelled, one former official said some feared that Zawahiri had cancelled the subway attack because Al Qaeda was planning something even more deadly and spectacular inside the United States—an event that, if planned, so far has not materialized.
Maybe they didn't want Bush to be re-elected. They were hoping for a Dem, and then they would carry out their attack.