Far from the prestigious windowed offices on the outer ring of the Pentagon, a new war room focusing entirely on the conflicts in Afghanistan and Pakistan sits deep inside a cavernous basement. Created by Navy Adm. Michael G. Mullen, the chairman of the Joint Chiefs of Staff, the Pakistan Afghanistan Coordination Cell is intended to bring together the Pentagon's top strategy and intelligence experts. The cell is also a visible symbol of how much the related conflicts have become Mullen's war. By law, the chairman of the Joint Chiefs has no official power to directly oversee troops. Still, Mullen's hand can be seen throughout the new U.S. military strategy for the two countries. He has repeatedly reminded military services of the Obama administration's sense of urgency. And he has brought an assertive approach, pushing them to shift their best officers and key equipment to the region. In December 2007, a couple of months after becoming chairman of the Joint Chiefs, Mullen offered a searing critique of U.S. war policy: "In Afghanistan, we do what we can. In Iraq, we do what we must." Later, he established the now-conventional wisdom in Washington that the fates of Afghanistan and Pakistan are irrevocably linked, and he commissioned a staff review that became a cornerstone of the Obama administration's strategy for the region. The new strategy includes sending 21,000 additional U.S. troops to Afghanistan. But it also makes a much deeper commitment to counterinsurgency. To implement it, Mullen worked with Defense Secretary Robert M. Gates to oust the previous U.S. commander in Afghanistan, Army Gen. David D. McKiernan. Mullen's top aide, Army Gen. Stanley A. McChrystal, was installed in his place. McChrystal has put in place tough new rules backed by Mullen aimed at minimizing civilian casualties and is emphasizing that the military's priority is protecting civilians, not killing insurgents -- even if that means some areas of Afghanistan remain under Taliban control for the time being. Military officials say Mullen has not just been moving top officers to Afghanistan, but has also been spurring the services to make changes deeper in the ranks. Mullen has demanded that officers graduating from the National Defense University prepare to deploy to Afghanistan. Previously, these officers would often get staff jobs in the Pentagon or other military commands. But Mullen wants the university's best students to fill key vacancies in Afghanistan. "He has made clear that Afghanistan is where he needs his 'A' team right now," said a military officer. Mullen's influence over the Afghanistan campaign contrasts with his predecessors, Marine Gen. Peter Pace and Air Force Gen. Richard B. Myers, who wielded little public influence over the conduct of the wars in Iraq and Afghanistan. When it came time to overhaul the Iraq effort, outsiders outflanked the Joint Chiefs. The shift is undoubtedly due to the fact that Gates is more comfortable with military leaders taking a public role in shaping and explaining war strategy than was his predecessor, Donald H. Rumsfeld. But Mullen also was chosen by Gates because he had a wider view of the military's problems and the drive to solve them, according to current and retired military officers. "What I have seen Adm. Mullen do in the last year, 18 months is take far more ownership of the war in Afghanistan and success in the outcome there than any of his predecessors," said David W. Barno, a retired Army lieutenant general who led the military command in Afghanistan from 2003 to 2005. James L. Jones, the White House national security advisor, has praised Mullen's effectiveness as chairman of the Joint Chiefs, and Gates has noted his "visible role." "He was very sensitive about not being able to resource Afghanistan in the way we needed to earlier," Gates said. "That is one of the reasons he is focused on making recommendations and taking actions that give us as good a chance as possible." Mullen is not an especially eloquent speaker. He frequently leaves sentences unfinished, moving quickly from thought to thought. But he has the power of the bully pulpit, and is often called to testify before Congress. He also wields power as an advisor to Gates and the president. Roughly half of the recommendations adopted by the White House in its review were originally from the strategy review ordered by Mullen -- including the idea of looking at Afghanistan and Pakistan as an interrelated problem. One of the architects of the shift in Iraq strategy in 2007 -- temporarily increasing the number of troops to improve security -- was Army Gen. David H. Petraeus, who took the lead in explaining it. 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." (L A Times)