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CAMPBELL BROWN: Now a CNN exclusive. It is the product of a lot of hard work by 360's Michael Ware and his Baghdad bureau colleagues. For the last two weeks they've been digging through a mother lode of documents and video from hard drives seized by U.S. allied Iraqi militias.

The material opens a remarkable window on the inner workings of al Qaeda in Iraq. It also tells the story of its undoing.

A warning, though: as welcome as that story may be, it is also terribly hard to watch.

Here's Michael's report.

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MICHAEL WARE, CNN CORRESPONDENT (voice-over): Al Qaeda gunmen brought this man here to die. Staged for maximum impact, he's to be executed on this busy market street. We don't know why. The al Qaeda members who recorded this tape offer no explanation. But the anticipation is agonizing, leading to a moment we cannot show you.

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WARE: A punishment for betraying al Qaeda? Or for breaking their strict version of Islamic law? Either way, it was public executions like this that would help lead to the unraveling of al Qaeda in Iraq, and al Qaeda knew it. Its leaders recognized their greatest threat was not the U.S. military, but the men in the crowds who witnessed the slaughters and who would eventually turn against them.

In fact, in this secret memo three years ago, a senior al Qaeda leader warned against a backlash for the public executions. They were being carried out, he wrote, "in the wrong way, in a semi-public way, so a lot of families are threatening revenge, and this is now a dangerous intelligence situation."

But U.S. intelligence did not pick up on this weakness for more than a year. Most of these men were once insurgents. Some even members of al Qaeda. But now they're on the U.S. government payroll, paid to assassinate al Qaeda.

All of these secrets come from here, the town of Ramadi. Al Qaeda computer hard drives were discovered here when one of these U.S.-backed militias overran an al Qaeda headquarters. As for the al Qaeda members, they showed them no mercy.

Eventually, the secret hard drives were passed along to both the U.S. military and to CNN.

Until recently, this man, Abu Saif, was a senior al Qaeda commander. He's now changed sides and confirms these are genuine al Qaeda in Iraq documents. Documents that reveal a network that's sophisticated, well-organized, meticulously bureaucratic and thorough.

Rear Admiral Patrick Driscoll is the U.S. military spokesman in Iraq.

REAR ADMIRAL PATRICK DRISCOLL, SPOKESMAN, MULTINATIONAL FORCE: Well, it's kind of unique what you have, because you have a comprehensive snapshot of al Qaeda at a time where it was a network or a unit.

WARE: In one local headquarters alone, more than 80 execution videos were cataloged. Not for propaganda. They were never made public. But as proof of killings for al Qaeda's superiors.

DRISCOLL: I was kind of surprised when I saw the degree of documentation for everything. Pay records, those kind of things.

WARE: In addition to pay sheets, hit lists and membership application forms, there are detailed lists of prisoners held, tried and executed. And then this: architectural schematics for storage bunkers on a U.S. base, proof al Qaeda has infiltrators inside America's compounds.

And despite the administration's insistence al Qaeda in Iraq is dominated by outsiders, in the secret correspondence obtained by CNN, the orders are given by Iraqis. Non-Iraqi fighters are used mostly in frontline roles, such as suicide bombings.

And these pages contain a complex strategy for planning and executing a three-month wave of simultaneous al Qaeda attacks.

DRISCOLL: When you're talking about an organization that's a network of networks, it's pretty resilient. And there are still determined elements in the al Qaeda hierarchy that want to win in Iraq.

WARE: Win to restore their own harsh justice. Here, al Qaeda gunmen punishing thieves, dangling them from an overpass and shooting them from below. While al Qaeda today no longer wields this power, the U.S. military is wary of its return.

DRISCOLL: A threat of al Qaeda, if not watched carefully, and not pursued aggressively, will come back and be the largest threat.

WARE: Though al Qaeda in Iraq is now under pressure as never before, these documents and videos warn its threat is more organized and more menacing than many ever imagined. After all, al Qaeda remembers when not so long ago it was welcomed by waving children.

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BROWN: And Michael Ware joining us now live.

And Michael, how relevant do you think al Qaeda is in Iraq today? Are they still a threat on any level?

WARE: Yes, they certainly are, Campbell.

Now, this war may really be a war of contests between Washington and Tehran for influence here in Iraq and in the region. But al Qaeda in Iraq is still very much a player in that.

Al Qaeda only comprises a small part of the insurgency. But we've seen over, say, the past ten days, just for example, al Qaeda in Iraq was still able to pull off six suicide bombings and three truck bombings, in which, one of these attacks, American soldiers were killed -- two American soldiers were killed and 18 were wounded.

So very much al Qaeda is still out there. They're operating much more as a covert, underground network, unlike before, where they actually controlled large parts of this country. But nonetheless, they still remain resilient, and the U.S. military well knows its capacity to come back from the brink -- Campbell.

BROWN: All right. Michael Ware for us tonight from Baghdad. Michael, as always, thank you.

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The version that aired on Domestic on 6/12 had some slight editing changes in the video portion, so I have also saved the original version that aired on International the day before:

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