He also worked with the Pakistani government to establish a staging point from which Marines could move into Afghanistan. The government wanted to keep its involvement secret, Mattis said in 2006, so the U.S. troops worked only in the middle of the night at a civilian airstrip and hid their gear in nearby sand dunes during the day.

Iraq

Mattis returned to Iraq in 2003, when he led the 1st Marine Corps Division to Baghdad as part of Operation Iraqi Freedom. For 17 days, the division pushed from the Kuwaiti border to Baghdad, in what the Marine Corps says was the longest sequence of overland attacks in its history.

By October 2003, the division had returned home; in November, Mattis was told that the Marines were going back to Iraq. In 2004, he led the first assault on Fallujah, one of the most pitched battles of the war. Later, he served as a senior negotiator and assured the city that the Marines had set aside $40 million to repair the city's damages.Still, he said later, "I was negotiating with people I'd rather have been shooting, to put it bluntly, because they were the enemy."

It was in Iraq that Mattis first started considering the counterinsurgency techniques that he and Gen. Petraeus would later write about. He was looking, he said later, for ways to "try and turn down the cycle of violence" in Iraq.

Field Manual 3-24

By the end of 2004, Mattis was back in America and serving at Quantico as the head of the 1st Marine Expeditionary Force. He pushed to extract lessons learned in the field and incorporate them on a regular basis into the force's work. He also pushed to create the Marine Infantry Immersion Simulator. "I went to the entry-level training of the Marine Corps and I was not satisfied that a couple of years into this war we were adapting fast enough," he told Esquire Magazine in 2006.

During this period, Mattis began working with Gen. Petraeus on Field Manual 3-24, the now infamous handbook for counterinsurgency operations. He also created the Center for Advanced Operational Cultural Learning, which provided language training and cultural education.

During his stint at Central Command, Mattis brought charges against Lt. Col. Jeffrey Chessani for the killing of 24 Iraqis in Haditha; Chessani's defense teams argued that the decision was politically motivated. Mattis said in 2008 that he spent more time on this case than on any other issue during this period.

Joint Forces Command

In 2007, Mattis received his fourth star and took over Joint Forces Command, which helps coordinate operations and activities that cut across military branches. Mattis has said that each branch of the military has unique strengths that can be relevant at different historical moments. "I don't want a joint culture that subsumes the Army, Navy, Air Force and Marines. I want them each to have their own and for us to harvest the good out of all of them," he said.

Mattis' tour at JFCOMM was scheduled to end in 2010, and many military observers thought he could be the next Marine Corps commandant. He was passed over for that job and had begun talking about retirement. After Gen. Petraeus left CENTCOM to take charge of the war in Afghanistan, however, Mattis was nominated as his replacement.

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