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When David Petraeus walks into the Central Intelligence Agency today, he will be taking over an organisation whose mission has changed in recent years from gathering and analysing intelligence to waging military campaigns through drone strikes in Pakistan, as well as in Yemen and Somalia.

But the transformation of the CIA did not simply follow the expansion of the drone war in Pakistan to its present level. CIA Director Michael Hayden lobbied hard for that expansion at a time when drone strikes seemed like a failed experiment.

The reason Hayden pushed for a much bigger drone war, it now appears, is that it had already created a whole bureaucracy in the anticipation of such a war.

During 2010, the CIA “drone war” in Pakistan killed as many as 1,000 people a year, compared with the roughly 2,000 a year officially estimated to have been killed by the SOF “night raids” in Afghanistan, according to a report in the Sep. 1 Washington Post.

A CIA official was quoted by the Post as saying that the CIA had become “one hell of a killing machine”, before quickly revising the phrase to “one hell of an operational tool”.

The shift in the CIA mission’s has been reflected in the spectacular growth of its Counter-terrorism Center (CTC) from 300 employees in September 2001 to about 2,000 people today – 10 percent of the agency’s entire workforce, according to the Post report.

The agency’s analytical branch, which had been previously devoted entirely to providing intelligence assessments for policymakers, has been profoundly affected.

More than one-third of the personnel in the agency’s analytical branch are now engaged wholly or primarily in providing support to CIA operations, according to senior agency officials cited by the Post. And nearly two-thirds of those are analysing data used by the CTC drone war staff to make decisions on targeting.

Some of that shift of internal staffing to support of the drone has followed the rise in the number of drone strikes in Pakistan since mid-2008, but the CIA began to lay the institutional basis for a bigger drone campaign well before that.

Crucial to understanding the role of internal dynamics in CIA decisions on the issue is the fact that the drone campaign in Pakistan started off very badly. During the four years from 2004 through 2007, the CIA carried out a total of only 12 drone strikes in Pakistan, all supposedly aimed at identifiable high-value targets of Al-Qaeda and its affiliates.

The George W. Bush administration’s policy on use of drones was cautious in large part because the President of Pakistan, Gen. Pervez Musharraf, was considered such a reliable ally that the administration was reluctant to take actions that would risk destabilising his regime.

Thus relatively tight constraints were imposed on the CIA in choosing targets for drone strikes. They were only to be used against known “high-value” officials of Al-Qaeda and their affiliates in Pakistan, and the CIA had to have evidence that no civilians would be killed as a result of the strike.

Those first 12 strikes killed only three identifiable Al-Qaeda or Pakistani Taliban figures, But despite the prohibition against strikes that would incur “collateral damage”, the same strikes killed a total of 121 civilians, as revealed by a thorough analysis of news media reports.

A single strike against a madrassa on Oct. 26, 2006 that killed 80 local students accounted for two-thirds of the total of civilian casualties.

Despite that disastrous start, however, the CIA had quickly become deeply committed internally to building a major programme around the drone war. In 2005, the agency had created a career track in targeting for the drone programme for analysts in the intelligence directorate, the Sep. 2 Post article revealed.

That decision meant that analysts who chose to specialise in targeting for CIA drone operations were promised that they could stay within that specialty and get promotions throughout their careers. Thus the agency had made far-reaching commitments to its own staff in the expectation that the drone war would grow far beyond the three strikes a year and that it would continue indefinitely.

By 2007, the agency realised that, in order to keep those commitments, it had to get the White House to change the rules by relaxing existing restrictions on drone strikes.

That’s when Hayden began lobbying President George W. Bush to dispense with the constraints limiting the targeting for drone attacks, according to the account in New York Times reporter David Sanger’s book “The Inheritance”. Hayden asked for permission to carry out strikes against houses or cars merely on the basis of behaviour that matched a “pattern of life” associated with Al-Qaeda or other groups.

In January 2008, Bush took an unidentified first step toward the loosening of the requirements that Hayden sought, but most of the restrictions on drone strikes remained in place. In the first six months of 2008, only four strikes were carried out.

In mid-2008, however, Director of National Intelligence Mike McConnell returned from a May 2008 trip to Pakistan determined to prove that the Pakistani military was covertly supporting Taliban insurgents – especially the Haqqani network – who were gaining momentum in Afghanistan.

A formal assessment by McConnell’s staff making that case was produced in June and sent to the White House and other top officials, according to Sanger. That forced Bush, who had been praising Musharraf as an ally against the Taliban, to do something to show that he was being tough on the Pakistani military as well as on the Afghan insurgents who enjoyed safe havens in northwest Pakistan.

Bush wanted the drone strikes to focus primarily on the Afghan Taliban targets rather than Al-Qaeda and its Pakistani Taliban allies. And according to Sanger’s account, Bush quickly removed all of the previous requirements for accurate intelligence on specific high-value targets and for assurances against civilian casualties.

Released from the original constraints on the drone programme, the CIA immediately increased the level of drone strikes in the second half of 2008 to between four and five per month on average.

As Bob Woodward’s account in “Obama Wars” of internal discussions in the early weeks of the Barack Obama White House shows, there were serious doubts from the beginning that it could actually defeat Al- Qaeda.

But Leon Panetta, Obama’s new CIA director, was firmly committed to the drone war. He continued to present it to the public as a strategy to destroy Al-Qaeda, even though he knew the CIA was now striking mainly Afghan Taliban and their allies, not Al-Qaeda.

In his first press conference on Feb. 25, 2009, Panetta, in an indirect but obvious reference to the drone strikes, said that the effort to destabilise Al-Qaeda and destroy its leadership “have been successful”.

Under Panetta, the rate of drone strikes continued throughout 2009 at the same accelerated pace as in the second half of 2008. And in 2010 the number of strikes more than doubled from 53 in 2009 to 118.

The CIA finally had the major drone campaign it had originally anticipated.

Two years ago, Petraeus appeared to take a somewhat skeptical view of drone strikes in Pakistan. In a secret assessment as CENTCOM commander on May 27, 2009, which was leaked to the Washington Post, Petraeus warned that drone strikes were fueling anti-U.S. sentiments in Pakistan.

Now, however, Petraeus’s personal view of the drone war may no longer be relevant. The CIA’s institutional interests in continuing the drone war may have become so commanding that no director could afford to override those interests on the basis of his own analysis of how the drone strikes affect U.S. interests.

Gareth Porter is an investigative historian and journalist with Inter-Press Service specialising in U.S. national security policy. The paperback edition of his latest book, “Perils of Dominance: Imbalance of Power and the Road to War in Vietnam“, was published in 2006.