I’ve been thinking about this quite a bit. Isn’t the most charitable explanation for all sides something like this:

Clarke banged his head against the wall about al Qaeda for years in the Clinton administration. He made significant headway in convincing his superiors of the threat if not necessarily the proper response to it. When the Bush team took over, Clarke stayed on but he was tainted by precisely that failure on the part of the Clintons to respond to terrorism. In the Bush White House he was not only a holdover who’d been demoted, but a one-note-Johnny. His one note might have been a good one, but he was unwilling to rethink foreign policy priorities the way the new guys wanted. When he was told to take a fresh look at Iraq, he bristled. He’d been working on this for years after all and his predictions of an al Qaeda attack had just come true, demonstrating in gory detail his failure to make his case successfully. Meanwhile, Bush — during a huge foreign policy crisis — didn’t need the attitude from Clarke and he may have misinterpreted Clarke’s reluctance also. So the Commander-in-Chief gave his instructions in a very forcefull way which Clarke misinterpreted as intimidation.

Now, just because this is the most charitable explanation doesn’t mean it’s the most likely. Frankly, if Clarke truly believed that Bush was looking for manufactured evidence of Iraq’s complicity he should have resigned in a very public way. Indeed, if he thought the Clinton administration’s failure to strike al Qaeda was as ill-advised as he’s indicated in the past, he should have resigned in the 1990s.