In the end, President Obama was forced to listen to his generals — not his political instincts — on Afghanistan troop levels, and he decided to split the difference.

Mr. Obama is keeping 5,500 troops in Afghanistan beyond his presidency, about half the strength recommended by his top general in-country. It marks the sixth time he has rejected the advice of a ground commander on the force size in the long Iraq and Afghanistan wars. Military experts call that streak unprecedented for a commander in chief.

Like the current 9,800 U.S. troops there, the drawdown force of 5,500 will maintain a noncombat stance in training Afghan forces and hunting al Qaeda terrorists, Mr. Obama said Thursday. Administration officials said the U.S. will spend about $14.6 billion a year to house the troops at a total of four bases in Kabul, Kandahar, Jalalabad and Bagram — an increase over the estimated $10 billion annual cost of keeping a force at the U.S. Embassy in the Afghan capital.

The president had wanted to deliver a speech saying that all American troops were out of Afghanistan at the end of next year, as he did in 2011 for the U.S. withdrawal from Iraq. But he was swayed by the dark picture of the Afghan conflict that the top brass has been drawing for him, and now Mr. Obama will pass the war onto the next president in 2017.

The battlefield facts delivered to the White House by Army Gen. John Campbell, the top NATO commander in Afghanistan, and other generals:

• The Taliban mounted a ferocious offensive in the 2015 “fighting season” that took a heavy casualty toll on the shaky Afghan National Security Forces.

• Those forces still lack competent leaders to win decisive battles without American troops to guide them.

• A new enemy has emerged, the ultraviolent Islamic State (also known as ISIL or ISIS) in a province next door to Kabul, the Afghan capital. This confronted the elected government with new security threats, especially the terrorist army’s trademark vehicle-borne improvised explosive devices.

“The security situation in Afghanistan is so far from stable that to pull out all the troops, even for this president, doesn’t make any sense,” said retired Army Gen. John Keane, who devised the 2007 Iraq troop surge and has advised Afghan commanders in the past.

Mr. Keane, whose guidance is sought by Congress, said Gen. Campbell wanted to retain the current force of 9,800, but Mr. Obama “cut that in half.”

“He still does not listen to his combat field general, who wanted the current force to remain as is,” Mr. Keane said. “Quite unprecedented, this is the sixth time President Obama has not listened to a field commander recommendation on force levels for troops in combat.”

The six times: Mr. Obama rejected a recommendation from Army Gen. Lloyd Austin, chief of U.S. Central Command, to keep about 20,000 troops in Iraq; at five transition points in Afghanistan, he approved troop numbers below those urged by commanders.

Still, Mr. Obama did compromise on troops and infrastructure instead of ordering the complete withdrawal he had wanted.

“The goodness in this decision are the four bases,” Mr. Keane said. “If he had reduced it to one base, which they were thinking of doing, that would be a disaster.

“The four bases permits the military to conduct counterterrorism operations in the east, south and in vicinity of the capital, which is absolutely critical, one of the crucial capabilities we lost when we pulled all troops out of Iraq,” he said. “Also, the four bases permits the next president to expand the troop presence rapidly based on the security situation 15 months from now.

“What suffers as a result of this decision is the train-and-assist mission, because we won’t have sufficient troops to do it properly,” the retired general said.

‘A wise decision?’

Train-and-assist is one of three major missions now carried out by American forces. The other two: advise and accompany Afghan forces on counterterrorism operations and provide force protection.

On Thursday, the administration defended the president against criticism that he ignored the advice of his top military advisers, with White House press secretary Josh Earnest saying that Mr. Obama’s decision is “consistent with” Gen. Campbell’s recommendation.

It is likely that Gen. Campbell’s communications with the White House in recent months mirrored the somber report he delivered Oct. 6 to the Senate Armed Services Committee.

There he spoke of a “struggling” Afghan force that faced its longest fighting season as the Taliban began early — in February. In the east, the Islamic State “further complicated the theater landscape and potentially expanded the conflict,” Gen. Campbell said.

All the while, he said, the Afghans lacked the robust U.S. air power they had come to rely on to arrive on the scene in minutes and deliver precision fire. Such air support “is no longer the norm but the exception,” he said.

The commander’s report card on the Afghan force: “They must improve their intelligence fusion, command and control utilization of their forces. They don’t possess the necessary combat power and numbers to protect every part of the country. This makes it very difficult for the Afghan security forces to counter the Taliban’s ability to temporarily seize an objective and then blend back into the population.”

Marine Corps General Joseph Dunford, the new chairman of the Joint Chiefs of Staff, is now Mr. Obama’s chief military adviser.

During his July confirmation hearing before the Senate Armed Services Committee, Gen. Dunford all but broke with the president’s then-desire to pull all troops out by the end of 2016. One could extrapolate from his answers to questions from committee Chairman John McCain, Arizona Republican, that he would attempt to talk the president out of that plan.

“Is this a wise decision on your part to have a calendar-based withdrawal of American troops rather than a condition-based withdrawal given your background and experience there?” Mr. McCain asked Gen. Dunford, a former Afghan NATO commander.

“I’m aware of the consequences of our mission and importance of our mission in Afghanistan,” the general answered. “I can assure you, if I’m confirmed, I’ll provide advice to the president that will allow us to meet our desired end state. And I think that that will be based on the conditions on the ground, as you’ve articulated.”

Mr. McCain said Thursday “it makes no military sense to withdraw U.S. forces” below the current 9,800.

“Once again, President Obama is putting our mission in Afghanistan, as well as our men and women serving there, at greater risk, and he is doing so for the sake of a troop reduction that has no political benefit but could have significant military implications,” he said.

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