The most startling finding of the 9/11 commission’s interim report this week was their denial that hijacker Mohammed Atta’s met in Prague with an Iraqi intelligence officer. In itself, the story does not make Saddam Hussein the mastermind of the attacks, but it’s an important reminder of the vast network of contacts between Saddam’s Iraq and Osama bin Laden’s jihadists.

It also tells us exactly what’s wrong with the 9/11 commission. Let me start with what I know.

Atta was twice in Prague, and on at least one of those occasions, on April 6, 2001, he met with an Iraqi diplomat. This was already his second visit, the first one, in extremely bizarre circumstances, involved flying to Prague without a visa in 2000, spending five hours at the airport, skillfully avoiding the airport cameras, returning to Germany and heading right back to Prague again (visa number BONN200005260024, according to investigative reporter Edward Epstein). He then headed to Florida.

On the second visit, Atta seems to have traveled to the scenic Czech capital solely to meet a shady Iraqi, Ahmed Ibrahim Samir al-Ani, who was already being followed by the Czechs on account of his undiplomatic activities. The Czechs had little doubt that Mr. al-Ani, the second consul at the Iraqi mission, spent more time organizing an Arab espionage network in Prague than stamping passports. Mr. al-Ani’s network of Arab informants were poking around the American funded Radio Free Iraq and mingling in the Arab community. But what the Czechs couldn’t decide was how serious of a threat Mr. al-Ani was – a mere ankle-bite of a spy sent to lure the government in Prague into an embarrassing diplomatic spat with Baghdad or a serious sponsor of terrorism. Senior officials at the time guessed it was more likely the first.

A meeting with an Arab student gave the situation a new light. Though no one was able to listen in on the dinner conversation, the Czechs had received tips “from a friendly country” on his visit that the student, none other than Atta, was of a dangerous sort. Later that month, fearful of an Iraqi organized attack on the Radio Free Iraq, they expelled Mr. al-Ani – with an urgent warrant forcing him to leave on a weekend – to nearby Austria. Being good allies, they also let the American authorities and the FBI know about the Iraqi spy’s expulsion.

So much I was able to gather in the months after the attacks from senior Czech officials who have worked on the case. The Czech government is confirming the meeting. It came forth the week after September 11 and told Washington what it knows.

How, then, to account for the uncanny conclusion of the 9/11 commission’s interim report which concluded the Prague meeting never happened, and that Iraq and Al Qaeda did not collaborate? The answer has something to do with the imprecise nature of intelligence gathering, but also with the partisan nature of the 9/11 saga.

Take, for example, the situation of the Czechs, who figured out soon after 9/11 the extent to which American intelligence agencies would go to discredit “inconvenient” findings. The Prague story was repeatedly discredited by anonymous intelligence sources in Newsweek and the New York Times, until George Tenet testified in February: “We can’t prove that one way or another.” The CIA and State Department’s efforts to prevent a war with Iraq were there. The Prague connection was an instant casus belli. Allies saw little reason to meddle in an all-American fight.

“The biggest political football,” a European diplomat once said describing the 9/11 investigation. The Czechs, like others, understood early on that the CIA and the FBI “did not want to know what they do not know.” Similarly, others had to weigh in on issues like who would be the next president, how the information could leak, whether it might ultimately be used to threaten the original source. There just were too many reasons to think twice before helping a deeply divided Washington solve the 9/11 puzzle. A shame.

That the 9/11 commission has not been able to rise above these epistemological problems that plague intelligence bureaucracy was the sad conclusion of last week. The link between Al Qaeda and Iraq is beyond doubt; one would hope the commission would force the boundaries of spy bureaucracy to deeper penetrate the heart of Middle Eastern terror networks. They could have at least used the safe Tenet line of not knowing “one way or the other” or pulled a Rumsfeldian about the “known unknowns” and “the unknown unknowns.”

Instead, they came up with a partisan document that reflects little innovative thinking on post-9/11 intelligence. It also shows no ability to look into the heart of tyranny.