WASHINGTON — For nine months, the Pentagon played down the presence of its 1,000 troops in Syria, hoping that President Trump would not focus on the extent to which the American military was continuing to fight the Islamic State despite his order in December to pull out.
On Sunday, the president appeared to say he had had enough.
Now, for the second time in less than a year, the Defense Department, the State Department, Congress and staff across the national security establishment are scrambling to respond to the words of a president who views Syria and the fight against ISIS as a battle largely won and done for American troops. On Monday, after a White House announcement the night before that Mr. Trump was moving American troops out of the way of a threatened Turkish incursion into Syria, Defense Department officials were struggling to put their already piecemeal Syria military strategy back together again.
It will not be easy. Caught between furious Kurdish allies who see Mr. Trump’s announcement as abandonment, an authoritarian Turkish leader who may take Mr. Trump’s words as tacit permission to move against Kurds in northern Syria, and an American president who has made clear he wants out of the region, the Pentagon is approaching a junction that the military feared was coming for some time.
The Defense Department “made lemonade out of lemons” the first time Mr. Trump announced a Syria withdrawal, said Derek Chollet, an assistant secretary of defense in the Obama administration. The Pentagon withdrew 1,000 of its 2,000 troops, moved some command elements to Iraq, and continued to aid Kurdish fighters still fighting the Islamic State and holding some 11,000 Islamic State prisoners of war.
But officials did not trumpet their mission or their efforts.
It will be a lot harder to pull this feint again, military experts said, particularly if President Recep Tayyip Erdogan of Turkey goes ahead with his threatened incursion into northern Syria, as it has been the presence of American troops alongside the Kurds that many believe has kept him at bay.
Pentagon officials were insisting on Monday that the United States remained firmly opposed to a Turkish incursion. “The Department of Defense made clear to Turkey — as did the president — that we do not endorse a Turkish operation in northern Syria,” Jonathan Hoffman, a Pentagon spokesman, said in a statement. He warned that “unilateral action creates risk for Turkey,” which would be responsible for thousands of Islamic State fighters being held by the Kurds.
But the departure of American troops from northern Syria makes it far more difficult to hold together the coalition fighting the Islamic State.
For a while, the generals at the Pentagon thought they were succeeding within the narrow confines of maneuver room that Mr. Trump gave them, obeying the president’s order while not deserting Kurdish partners and undercutting gains against the Islamic State in northeastern Syria. Defense Department officials devised a plan for the Pentagon to cut its combat force there roughly in half by early this past May, or to about 1,000 troops — and then pause with what commanders called a “residual force.”
The military would then assesses conditions on the ground and reduce the number of forces periodically, if conditions allowed, until the force levels reached the 400 troops that Mr. Trump approved in February.
And, above all else, military officials decided they would keep quiet about Syria. The strategy extended all the way to combat outposts in the country, where Special Forces officers were reminded that their mission could end quickly if the commander in chief was publicly reminded that there were still 1,000 troops there, according to one officer who recently returned from Syria.
The longer withdrawal timetable gave the Trump administration more time to negotiate with European allies who had said they would not leave troops in Syria if the United States withdrew all of its forces. It was also supposed to allow more time for Washington to work out details of a safe zone south of the Turkish border, where Mr. Erdogan wants to repatriate hundreds of thousands of Syrian refugees now in Turkey. Turkey also wants to make sure Kurdish fighters cannot launch terrorist attacks across its border.
By late March, the American withdrawal settled around 1,000 troops — what the military calls an “economy of force” mission. The troops effectively operated between two allies: Turkey and the Kurds. Turkey is a decades-long NATO partner. The Syrian Kurds are much more recent allies, but have played a pivotal role as the major ground force against the Islamic State.
The problem for Washington has been that the two hate each other.
After Mr. Erdogan threatened in early August to carry out a cross-border operation to attack the Syrian Kurds, American diplomats and commanders rushed to establish a series of confidence-building measures — joint reconnaissance flights and ground patrols by American and Turkish forces — along a 75-mile stretch of the 300-mile border east of the Euphrates River.
The American troops in northeastern Syria, largely teams of Special Forces, also provide important logistics, intelligence and other support for Syrian Kurdish fighters who continue to carry out raids and disrupt operations against Islamic State targets.
Since the American-backed forces ousted the Islamic State from its last shard of territory in Syria seven months ago, the terrorist group has been gathering new strength, officials say, conducting guerrilla attacks across Iraq and Syria, retooling its financial networks and targeting new recruits at a giant allied-run tent camp in northeastern Syria called Al Hol.
“After enlisting support from the Kurds to help destroy ISIS and assuring Kurdish protection from Turkey, the U.S. has now opened the door to their destruction,” Senator Mitt Romney, Republican of Utah, and Senator Christopher S. Murphy, Democrat of Connecticut, said in a statement on Monday. “This severely undercuts America’s credibility as a reliable partner and creates a power vacuum in the region that benefits ISIS.”
Pentagon officials say the American presence, and several million dollars in assistance to maintain and upgrade the Syrian Kurds’ makeshift jails in northeastern Syria, has ensured the Kurds continue to detain about 11,000 ISIS fighters, including more than 2,000 foreigners.
“It’s hard to imagine Turkey has the capacity to handle securely and appropriately the detainees long held by the Syrian Kurds — and that’s if Turkey even genuinely intends to try,” said Joshua A. Geltzer, a former senior director for counterterrorism on the National Security Council in the Obama administration. “The release or escape of such detainees would instantly energize ISIS’s efforts, already underway, to regroup and surge again.”