Gordon Corera asks whether the US intelligence agency's methods are counter-productive

As was the case with so many other offices on that day, 11 September 2001 was full of confusion at CIA headquarters in Langley, Virginia. After watching transfixed as events unfolded on their TV screens, most staff were told to evacuate the building and go home. Many found themselves milling around in the car park as the roads near Langley jammed with traffic.

For some officers in the service, it was a chance to reflect on what appeared to be a significant failure. Wasn't this exactly the kind of event the CIA was supposed to stop? Some on the inside believe the organisation had lost its way in the 1990s, largely because the nemesis it had been founded to fight, the Soviet Union, had collapsed. On 12 September 2001 a tired looking George Tenet, the CIA director, addressed staff in the agency's auditorium. Whatever the past, the agency now had a clear mission - to defeat Al-Qaida - and it would pursue it relentlessly.

There would also be more relaxed rules, issued at the highest levels, about what kind of "techniques" could be used by the CIA in interrogating Al-Qaida detainees

Two days later, Cofer Black, the head of the CIA's Counterterrorist Center, summoned veteran officer Gary Schroen into his office. Schroen was about to retire, but Black asked him to lead the first team into Afghanistan to build relations with those who would help the US overthrow the Taleban. Black made another request. He asked him to bring back Osama Bin Laden's head in a box.

Black is famous for his choice turn of phrase, but his request signalled that something deeper was going on. After a series of major scandals in the 1970s, the CIA had been told to clean up its act. The result was a spy agency the top priority of which appeared to be avoidance of trouble. Assassination was formally banned, as was anything else that could bring on a career-ending congressional investigation. Black was indicating that the period of caution was over. He would later tell Congress that, after 11 September, "the gloves came off".

Four and a half years later what that actually meant is only now emerging. As well as a less rigid line with regard to assassinating Al-Qaida's leaders, there would also be more relaxed rules, issued at the highest levels, about what kind of "techniques" could be used by the CIA in interrogating Al-Qaida detainees. Some of those detainees became "ghost prisoners", perhaps in secret prisons in Eastern Europe. Just as controversially, it has become clear that the CIA engaged in "extraordinary rendition", in which suspects were picked up in one country and transported to another that was more "physical" in its interrogation policy.

This was the new CIA. But now its tactics are coming increasingly under the spotlight. Who ordered them? Are they morally acceptable? Are they even that useful? Are they essential tools in the fight against the most committed of opponents? Or are they becoming counter-productive, undermining claims to the moral high ground as well as international alliances vital to the USA's War on Terror?

They're afraid that once the full story's out... there will be punishment... they're very concerned that their butts are not covered

Under the CIA's new director Porter Goss, the agency has continued to focus on rebuilding its core business of recruiting spies. "That means close-in access to the hard targets. That means a lot of risk," Goss explained in an interview before his appointment. "That means clandestine officers who know how to run agents into hard target areas." But the agency may well become better known for events like the kidnapping of an Islamic radical, Hassan Mustafa Osama Nasr, known as Abu Omar, on the streets of Milan, who was then flown to Egypt and allegedly tortured. For their alleged role in the affair, a raft of CIA officers have been named and indicted by Italian prosecutors.

Under pressure from a White House that wants results on one side and campaigning groups who are suspicious of its activities on the other, the CIA is caught in the political cross-fire. Even some of those who worked inside the Bush administration suspect that there is still more to be revealed. "I cannot believe that we've let it get to the depth that it has gotten to," says Larry Wilkerson, who was chief of staff to Secretary of State Colin Powell until recently. "I even have CIA people now who talk to me and say they're deeply concerned, because they're afraid that once the full story's out... there will be punishment. And they're very concerned that their butts are not covered."

The CIA is at the frontline of the USA's War on Terror. The once-secret agency is now a very public touchstone and symbol for that war. As a tempest swirls around it, how will its contribution be judged?