WASHINGTON — Days after President Trump’s abrupt decision to withdraw 1,000 American troops from Syria, Gen. Mark A. Milley, the chairman of the Joint Chiefs of Staff, saw a way to turn it around.

The businessman in Mr. Trump had focused on the Syrian oil fields that, if left unprotected, could fall into the hands of the Islamic State — or Russia or Iran. So General Milley proposed to a receptive Mr. Trump that American commandos, along with allied Syrian Kurdish fighters, guard the oil.

Today, 800 American troops remain in Syria.

“We’re keeping the oil,” Mr. Trump told reporters on Wednesday before his meeting with President Recep Tayyip Erdogan of Turkey. “We left troops behind, only for the oil."

That is a far cry from where Mr. Trump was last month, when he ordered the withdrawal of all American troops from northern Syria. But now, for the second time in less than a year, the Pentagon has softened the president’s initial decision.

“I credit Milley with convincing the president to modify his Syria decision,” said Jack Keane, the former Army vice chief of staff, who spoke several times with Mr. Trump and General Milley last month during the frenzied days of the president’s zigzagging Syria policy.

Nearly three years into the Trump presidency, the Pentagon is learning how to manage a capricious president whose orders can whipsaw by the hour. Top Defense Department officials have acquired their education the hard way, through Mr. Trump’s Twitter bullying of Iran and North Korea, letdown of allies in Syria, harsh attacks on the Atlantic alliance and public support for commandos the military has charged with war crimes. Mr. Trump, top Pentagon officials say, is unpredictable, frustrating and overly focused on spectacles like military parades.

But there is much these officials like about the president.

They are happy with the annual budget boost he gave them — to $716 billion this year from $585 billion in 2016 — and are pleased he has done away with what they considered micromanaging by Obama White House officials. Mr. Trump has also given commanders in combat zones a far freer hand to conduct raids. And among a big portion of the rank and file, those service members who mirror Mr. Trump’s conservative base, he remains very popular.

In many ways, the American military remains the part of the government most responsive to the president across a large and fractious administration, because civilian control of the armed forces is embedded in the Constitution and the psyche of every soldier. But for Mr. Trump, the other side of that coin is that the military respects the coequal branches of government, as Lt. Col. Alexander S. Vindman demonstrated in recent days when, against the wishes of the president, he testified in the House impeachment proceeding.

New Freedom, and New Fallout

Once Mr. Trump took office, he gave the Pentagon and military commanders more running room. He allowed the Pentagon to speed up decision-making so the military could move faster on raids, airstrikes, bombing missions and arming allies in Iraq, Syria and elsewhere. The Pentagon, after eight years of chafing at what many generals viewed as the slow decision-making and second-guessing by the Obama White House, at first embraced the new commander in chief.

But with the new freedom came repercussions. Mr. Trump deflected blame onto the Pentagon if things went wrong. After a botched raid in Yemen in January 2017, which led to the death of Chief Petty Officer William Owens, a member of the Navy SEALs known as Ryan, Mr. Trump appeared to blame the military — a stunning departure from previous presidents, who as commanders in chief have traditionally accepted responsibility for military operations that they ordered.

“They explained what they wanted to do, the generals, who are very respected,” Mr. Trump told Fox News after the raid. “And they lost Ryan.”

On another issue important to the Pentagon, Defense Secretary Mark T. Esper and the Army secretary, Ryan McCarthy, have reached out quietly to Mr. Trump in recent days to ask that he not interfere in several war crimes cases. Defense Department officials are concerned that presidential pardons could undermine discipline across the ranks. The Army, for instance, is prosecuting a Green Beret, Maj. Mathew L. Golsteyn, in the killing of a man linked to the Taliban in Afghanistan; Mr. Trump has indicated he may pardon him. “I do have full confidence in the military justice system,” Mr. Esper told reporters.

And in the case of Syria, the Pentagon gave Mr. Trump an unexpected gift in return: the American commando raid that led to the death of the Islamic State leader, Abu Bakr al-Baghdadi, which so elated the president that he tweeted the news as soon as American troops were out of harm’s way.

The next day, Mr. Trump triumphantly mentioned General Milley four times during his 48-minute news conference on the raid, calling him “incredible” for his work and thanking him by name before any other senior administration officials.

Commanders have also learned to carefully parse their comments, wary of having their words construed as subtle criticism of the president.

During a news conference, Gen. Kenneth F. McKenzie Jr., the head of the United States Central Command, declined to repeat Mr. Trump’s assertion that the Islamic State leader was “whimpering” before he detonated his suicide vest after American troops raided his compound.

But General McKenzie backed up Mr. Trump’s characterization of Mr. al-Baghdadi as a coward. “He crawled into a hole with two small children, blew himself up,” the general said. “So, you can deduce what kind of person it is based on that activity.”

Defense Department officials also make sure to speak more frequently about how important it is to get North Atlantic Treaty Organization allies in Europe to “pay their fair share,” echoing Mr. Trump’s more transactional view of how that alliance should proceed. By emphasizing payment, rather than simply saying that the Pentagon wants European governments to bolster their own internal military budgets — a more accurate description of NATO policy — American officials couch something they wanted anyway in language that will appeal to the president.

On the Korean Peninsula, the United States and South Korea have continued to conduct joint military exercises despite Mr. Trump’s announcement that such “war games” be suspended pending nuclear negotiations with North Korea. Stopping the exercises completely, Defense Department officials say, would hurt military readiness in the event the United States does end up at war with the North. The military now conducts them at a smaller scale level and no longer makes them public.

In Afghanistan, Gen. Austin S. Miller, the commander of the war effort there, is preparing to shrink the American presence. Mr. Trump has said he wants all the troops withdrawn, but has given no timetable. General Miller now has plans that could reduce the number of American forces in Afghanistan to 8,600 troops, from roughly 12,000 to 13,000 — a move, American officials say, that will allow Mr. Trump to say in his 2020 re-election campaign that he is bringing the troops home. But it will leave what commanders consider an adequate number on the ground.

Clashes Over Syria

The relationship between Mr. Trump and the military has been the most fraught over Syria policy.

The problems began last December, when Mr. Trump first tried to bring what were then 2,000 American troops home from Syria and Jim Mattis, his first defense secretary, resigned in protest. In the storm that followed — Republicans, Democrats and some of Mr. Trump’s own advisers said he was pulling out of the fight before the Islamic State was defeated for good — Mr. Trump backtracked and agreed to leave some 1,000 American forces. But over the past year, Pentagon officials let them operate almost in secret to avoid calling attention to the fact that Defense Department officials had talked the president out of his initial order.

In early October, after a phone call with President Recep Tayyip Erdogan of Turkey, Mr. Trump signaled he had had enough, and announced he was pulling out those remaining troops. Once again there was another outcry from Republicans, Democrats and Mr. Trump’s own national security advisers, who said he was paving the way for a Turkish offensive against the United States’ longtime allies, Kurdish fighters, who had carried the brunt of the fight against the Islamic State. In particular, the military did not want to abandon the Kurds.

“The idea of walking away from that sacrifice, that is something that really bothers,” said Representative Mac Thornberry, Republican of Texas and the ranking member of the Armed Services Committee. “You want to salute and follow the orders of the duly elected political authorities, but you also don’t want to betray the sacrifice of your comrades. That puts the military, at least their hearts, in a tough place.”

“The decision to betray the Kurds punches a huge hole in the current way we fight terrorists which is by, with and through allies,” said Representative Elissa Slotkin, a Michigan Democrat on the Armed Services Committee and a former senior Pentagon official.

General Milley, along with Mr. Esper, looked quickly at how to yet again make the case to Mr. Trump that American forces still had work to do in Syria. The military’s Central Command had drafted two alternate plans.

One proposal would have kept a small force to help control a small swath of the border between Iraq and Syria, about 10 percent of the area. Another option would try to keep control of a larger part of the country — more than half of the area the American and Kurdish fighters currently controlled.

But after Mr. Trump told General Milley he wanted to keep the oil fields, the Pentagon quickly “operationalized” a new plan wrapped around using American forces and their Kurdish allies to protect the oil and to keep it from falling into the hands of the Islamic State, officials said. From Brussels, where he was attending a NATO meeting, Mr. Esper was on the phone with General Milley completing details of the new plan.

General Milley, for his part, has been advised by friends to maintain a low profile, and not to appear to be contradicting Mr. Trump’s decisions or strategy. Known for long monologues, General Milley has also learned to be concise with Mr. Trump, offering clear opinions but allowing the president to dominate the conversation.

By the end of October, Mr. Trump was on board with the Pentagon plan. At Game 5 of the World Series, he was in one of the luxury boxes at Nationals Park surrounded by Republican members of Congress and top aides. The conversation turned to Syria.

Mr. Trump talked about how he was revising his plans for Syria, repeatedly telling lawmakers that American forces would remain there. Why? Because America was “keeping the oil.”

Senior military and Defense Department officials say that in some cases, it is simply a matter of talking in a way that will appeal to Mr. Trump, while prosecuting a similar national security policy as they did under President Barack Obama.

“The Pentagon has figured out that they can couch things to manage Trump’s biases in some ways,” said Derek Chollet, a former assistant secretary of defense in the Obama administration. “Don’t make it about saving the Kurds, make it about saving the oil.”

At the moment, the Pentagon is left trying to continue the strategy in a patchwork fashion, with General Milley’s move to keep American troops in Syria helping Kurdish fighters protect oil fields the latest piece.

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