As defined by his commander in chief, the mission of Defense Secretary Robert M. Gates for the last two years has been to win the war in Iraq

But beginning on Jan. 20, Mr. Gates’s mission will be to end the war in Iraq, assuming the Pentagon boss stays in his post under an agreement with a new commander in chief, President-elect Barack Obama.

That contrast might seem to leave Mr. Gates consigned to serious whiplash.

While Mr. Obama campaigned on a promise to withdraw all American combat brigades from Iraq within 16 months, or by May 2010, Mr. Gates has spent his time at the Pentagon arguing a Bush administration position that has opposed setting strict timetables for withdrawal.

“I would urge our nation’s leaders to implement strategies that, while reducing our presence in Iraq steadily, are cautious and flexible and take into account the advice of our senior commanders and military leaders,” Mr. Gates told Congress in September. “I would also urge our leaders to keep in mind that we should expect to be involved in Iraq for years to come, though in changing and increasingly limited ways.”

While that statement would appear to set Mr. Gates on a collision course with the president-elect, there have also been signs of a possible emerging consensus.

Already, Mr. Gates and senior American commanders are looking at how they can achieve significant force reductions in the next year — which would fulfill a campaign pledge of the new president.

And while Mr. Obama’s most heartfelt supporters in the antiwar movement may have heard “end the war” as a promise to end the American troop presence in Iraq in 16 months, the president-elect has spoken only of a timeline for withdrawing combat troops, not all American forces.

Fifteen American combat brigades are in Iraq, but the total number of American troops there amounts to the equivalent of more than 50 brigades, including forces there on missions to support, supply, transport, protect and care for the combat forces, and train and support the Iraqi security forces, which would be expected to continue at least through 2011.

There are points of clear agreement between Mr. Obama and Mr. Gates, with both saying that American force reductions in Iraq should allow more troops to be sent to Afghanistan. And early in his tenure at the Pentagon, Mr. Gates mounted a remarkable inside initiative to reverse Bush administration policy and close the American detention center at Guantánamo Bay, Cuba, although he was overruled.

The initiative to close Guantánamo certainly puts Mr. Gates in the camp of leading Democrats, including Mr. Obama. Mr. Gates has also been more in favor of dialogue with Iran than have been hard-liners in the Bush administration, although Mr. Gates notes that the United States has for decades been fruitlessly searching for Iranian moderates with whom to negotiate.

Even on Iraq, Mr. Gates arrived at the Pentagon in December 2006 with a goal of turning a polarizing war into a mission that was sustainable, both politically and militarily, and not a national-security crisis that threatened to break the military and rupture public support for American engagement overseas. Mr. Gates has declared that the direction of troop levels in Iraq has now been determined — downward — and all that is left to decide is the timing.

While Mr. Gates has said he does not favor a rash withdrawal from Iraq that would risk security gains, senior military officials say he has, at the same time, pushed back against the natural inclination of commanders to hold as many troops in place as long as possible, and has pressed for moving ahead with troop reductions.

To reach agreement on the text of a long-term status-of-forces agreement with the Iraqis now before the parliament in Baghdad, the Bush administration notably dropped its opposition to formal timelines. American combat forces must pull back from cities and villages to major bases by June 30, 2009, and all forces must be out by the last day of 2011.

In contrast, Mr. Obama wants all combat forces out about a year and a half earlier than the deadline of Dec. 31, 2011. Aides to the president-elect say he does not oppose the current draft of the status-of-forces agreement, as it puts both Iraq and the United States formally on a glide path to removing American troops.

Some Army planners predict that 30,000 to 50,000 — and as many as 70,000 — American troops will remain in support and training missions well into late 2011, and beyond, should the Iraqis invite them.

The coming Iraqi elections are a time of expected instability, with increased violence, and commanders do not want to surrender security gains made under the troop increase ordered by President Bush.

But commanders say that by partnering with Iraqi security forces, and turning over an increasing number of combat zones to them, they should be able to recommend further reductions next year, allowing an increase of troops to Afghanistan. Troop recommendations are now being drawn up by Gen. Ray Odierno, the senior commander in Iraq, and Gen. David H. Petraeus, who oversees the campaigns in both Iraq and Afghanistan.

On other issues of national security, Mr. Gates has pressed for placing two American missile defense bases in Europe to counter a potential Iranian attack, while Mr. Obama has been far more skeptical of missile defense financing over all.

And while the Bush administration remains eager to bring the former Soviet republic of Georgia into NATO, Mr. Gates, a longtime Kremlin watcher from his days at the Central Intelligence Agency, has cautioned more broadly against a rush to enlarge the alliance. He has said that “NATO is not a talk shop nor a Renaissance Weekend on steroids,” and that the alliance must be wary of bringing in nations that other members might not actually defend in case of war with Russia.