Now head of Central Command, Petraeus has a large role in forming the military strategy for Afghanistan and Pakistan. Although still visible, Petraeus' strategy role has been less public than Mullen's. But a senior Defense official said Petraeus and Mullen are "joined at the hip," talking daily and e-mailing throughout the day. At least every other day, the chairman has a formal video teleconference with Petraeus.
The two men, the official said, take particular pains to coordinate their work on Pakistan to make sure they are sharing information and insights as well as sending a consistent message to the Pakistani military leadership.
Mullen, a native of Los Angeles, began his military career as a young officer on a destroyer off Vietnam. Some think he has drawn lessons from that war.
"He is very sensitive about the importance of trying to do something about the enemy sanctuary in Pakistan," said a retired colonel. "He recognizes it is very analogous to what we experienced in the Vietnam War, with the enemy leveraging Laos and Cambodia."
Mullen has made more than a dozen trips to Pakistan, usually meeting with the army chief of staff, Gen. Ashfaq Kayani.
The long courtship appears to have paid dividends. Kayani, the former head of military intelligence, launched an offensive against Taliban militants this spring.
"We are very fortunate he and Gen. Kayani have developed a good relationship," Gates said.
Ahmed Rashid, a Pakistani journalist with whom Mullen consults regularly, says that until Mullen became Joint Chiefs chairman, the U.S. military was reluctant to confront Pakistani defense officials about their country's role in Afghanistan or to press them for more aggressive action against the Taliban.
"He is not a guy who brushes things under the carpet," Rashid said.
Some Defense officials think that besides trying to make a difference in the war effort, Mullen is intent on rebuilding the status of his job.
"He is an ambitious chairman," said another senior Defense official. "There is a conscious effort to reassert a position that has been diminished."
Rumsfeld allowed only limited public discussion of war strategy by the uniformed military, but some military officials said the Joint Chiefs under Pace did not do enough behind the scenes to challenge the Iraq strategy after it became clear it was failing.
The coordination cell in the basement of the Pentagon is one way to better focus on the challenges of Afghanistan.
Stripped of cubicle walls and lined with desks, the cavernous room with fluorescent lights looks something like an old-style newsroom or steno pool -- save for the addition of classified phones and computers at each workstation.
"Adm. Mullen understands the Pentagon has to change from planning wars to fighting them," said Army Maj. Gen. Michael T. Flynn, who served as Mullen's intelligence officer, then joined the command in Afghanistan.
The intent is to draw in experts on Afghanistan -- from all the military services as well as civilians -- who have experience in the country and expertise on Afghan politics, the insurgency, narcotics and other issues. The initiative will create a bench of experts who will eventually rotate back and forth between the U.S. and Afghanistan, a project McChrystal first began under the direction of Mullen.
Said Army Brig. Gen. Scott Miller, head of the coordination cell: "He understands it is going to take his personal involvement if we are not going to just do business as usual."
Times staff writer Doyle McManus in Washington contributed to this report.