At times, said one senior U.S. counter-terrorism official, Mohammed would travel to other countries to personally establish terrorist cells and provide them with plans for attack, money, manpower and logistical support. Other times, he would operate at a higher level, overseeing senior Al Qaeda commanders who led the attacks.
The official said Mohammed is believed to have been actively involved in the bombing of two U.S. embassies in Africa that killed 224 people in 1998, the bombing of the Cole in the Yemeni port of Aden in 2000, which killed 17 sailors and nearly sank the $1-billion U.S. warship, and many other attacks.
"There is a clear operational link between him and the execution of most, if not all, of the Al Qaeda plots over the past five years," the official said.
American investigators acknowledge that this evaluation of Mohammed as a central figure in Al Qaeda is largely retrospective. It wasn't until after Sept. 11 that his larger role became apparent.
"He popped up post 9/11 and then, looking back, we saw that he was the Zelig of Al Qaeda, involved in a lot of other things," one investigator said.
One of the hallmarks of Al Qaeda is its breadth, the dispersion of its resources. So, for example, parts of the network could be preparing to attack American warships in Yemen, others to bomb civilian targets in Europe and Asia, even as the larger organization was already planning Sept. 11.
In an interview with Al Jazeera television, recorded in May this year, Mohammed described himself as the head of Al Qaeda's military committee. He said that "about 2 1/2years prior to the holy raids on Washington and New York, the military committee held a meeting during which we decided to start planning for a martyrdom operation inside America."
That would date the inception of the plot to early 1999. Later that same year, the men who would execute it were chosen, he said. German intelligence agencies believe that Mohammed first came into contact with these men when they visited Al Qaeda camps in Afghanistan.
Several of the men were students in Hamburg, Germany, part of a small group of devout Muslims who were growing increasingly restive over the plight of the Islamic world.
They were largely middle class, some well educated, not dispossessed in any apparent way. One was an urban planner and architect, one an aeronautical engineering student and one a prospective marine engineering student. Mohammed, a mechanical engineering graduate, chose other engineers for Al Qaeda's riskiest undertaking. They were, like him, devout but at home in the West, adept at languages and technically inclined.
The rest of the hijacking crews were made up of two veteran Al Qaeda operatives, a replacement pilot and a group of young Gulf Arab volunteers, chosen from what Mohammed described as "a big excess of brothers who were filled with desire for martyrdom," whose job was mainly to effect the physical takeover of the airliners.
As Sept. 11 approached, intelligence agents in the West were nearly beside themselves with anxiety. They knew something was going to happen, but they couldn't figure out what. Mohammed was already moving on. He spent the weeks before Sept. 11 instructing a new Canadian recruit on communications protocols. He was sending the recruit to Southeast Asia to coordinate a bombing campaign in the Philippines and Singapore. The only acknowledgment that something big was afoot was his suggestion that the recruit should probably leave Pakistan before Sept. 11.
It is that sort of unrelenting focus that makes Mohammed such a feared figure among those who pursue him. He simply does not stop.
In the months after Sept. 11, investigators think that Mohammed was moving back and forth between Pakistan and Afghanistan. One Afghan general, Ziaudeen Deldar, said intelligence reports indicate that "Khalid the Baluchi" was among hundreds of Al Qaeda fighters who escaped on foot to Pakistan from a camp near Shahi Kot in southeastern Afghanistan last spring when American forces launched Operation Anaconda -- an attempt, they said, to finish off Al Qaeda.
Instead, the Americans faced considerably more resistance than anticipated and backed off. The grasp of the anaconda relaxed and the prey, including Mohammed, slipped away. Weeks later, Al Qaeda operatives blew up a truck outside a synagogue in Tunisia, killing 19 people. In the days leading up to the attack, investigators say, one of the bombers was in frequent telephone contact with a man in Karachi -- Mohammed.
Mohammed was accompanied at the Al Jazeera interview by Ramzi Binalshibh, another Hamburg man who had wanted to become one of the suicide pilots but who tried and failed four times to obtain a U.S. visa. Binalshibh instead became Mohammed's field coordinator for the plot.
It's noteworthy that in the interview, Mohammed let Binalshibh do most of the talking. Even in granting an interview, the purpose of which ostensibly was to reveal, he exposed almost nothing.
Karachi: Behind Walls