Gen. John Nicholson, center, during the change of command ceremony in Kabul, Afghanistan, on Sunday.Credit Credit Massoud Hossaini/Associated Press
KABUL, Afghanistan — When American Airlines Flight 77 struck the Pentagon on the morning of Sept. 11, 2001, Lt. Col. John W. Nicholson Jr. survived by chance. That morning, as dozens of his colleagues were killed, he was moving house and wasn’t at his desk — which he said was 100 feet from the nose of the plane.
Nearly 17 years to the day, now a four-star general departing as the commander of the American and NATO forces in Afghanistan, he stood under the shade of pine trees in Kabul on Sunday, and delivered an emotional farewell.
The general, who spent 31 months at the helm of a quagmire of a mission that has shaped his career over four tours of the country and has cast a shadow on a generation of American military leaders, said he wanted to speak from the heart.
“It is time for this war in Afghanistan to end,” General Nicholson said.
The general called on the Taliban to “stop killing your fellow Afghans,” but he also referred indirectly to regional players — particularly Pakistan, where the militants enjoy sanctuary — who have complicated the fight.
“Whose voices are important?” he asked. “The outsiders who are encouraging you to fight, or the voices of your own people who are encouraging you to peace?”
Naming the first and the last American soldier killed under his command and praying for the hundreds in between, the general demonstrated little of the chest-thumping of previous commanders and put aside his own sometimes rosy assessments of the situation for a more of a somber reality that seems to be dawning on the American military leadership.
He sought to provide a reminder about why the United States was in Afghanistan in the first place, a narrative that is increasingly lost on much of the public.
The war has dragged on so long that it is now fought by a generation of soldiers too young to remember the day when planes flown by members of Al Qaeda, which had found protection in Afghanistan under the Taliban, struck the World Trade Center and the Pentagon.
Then, General Nicholson, 61, echoed a call to immediately begin peace negotiations, an approach that has become an American priority that the Trump administration hopes will allow it to diminish its presence in the country, while also warning the Taliban that the United States would continue to fight.
His departure comes as the war seems to spiral deadlier even as it recedes from American attention — General Nicholson did not meet once with President Trump in the 20 months since he moved into the White House.
“Our soldiers are volunteers, permitting the American people and their elected representatives to be indifferent about the war in Afghanistan,” said Karl Eikenbery, a former commander of the American forces in Afghanistan who later served as the United States ambassador to Kabul. “We continue to fight simply because we are there.”
Like his predecessor, John F. Campbell, General Nicholson is likely to retire immediately, a diplomat with ties to the general said, a sign that the posting is no longer a springboard to more senior roles, and what appears to be the final chapter of his career encapsulates the trajectory of a 17-year war.
The United States’ involvement has moved from a wounded nation’s quest to strike back against the Taliban for facilitating Al Qaeda, to what critics say was a show of military hubris that sent young Americans deep into Afghan villages where the Taliban often had an advantage, to a desperate search for a dignified resolution, its urgency heightened by the unpredictability of an American president who has made no secret of his weariness for the war.
General Nicholson’s four tours of the country, in which he developed a personal commitment and an emotional attachment to the place and its people, also speaks to the toll of the conflict on the men and women who fought there.
He led the effort at a difficult time, when the Taliban had cranked up the pressure on the nascent Afghan forces taking the lead in the fight and when the political leadership in Kabul remained in disarray.
During his tenure, the longest by an American commander, he helped double the size of the Afghan special forces and triple that of the country’s air force. But he and his fellow generals tout a temporary rare cease-fire in June as a major success under his watch, a reflection of how much the goals and expectations of the American military have changed.
Mr. Eikenberry said that unlike his generation, many of the military leaders who began at the tactical level in the wars immediately after Sept. 11 had grown skeptical of waging comprehensive counterinsurgency warfare in a distant foreign lands.
But they continue to play large roles, in a war that only grows more complicated. “Warrior-diplomat” is how Gen. Joseph L. Votel, the most senior American military leader at the ceremony in Kabul, described General Nicholson.
“Military commanders in Afghanistan, absent political guidance and a diplomatic strategy, have filled the vacuum by waging a war all agree cannot be won militarily,” Mr. Eikenberry said. “Their mission has been to ‘make progress,’ which they themselves define and which is often unrelated to the tasks of delivering a sustainable peace and the withdrawal of U.S. forces.”
General Nicholson will be replaced by Gen. Austin “Scott” Miller, who left the shadowy Joint Special Operations Command to take on the war effort of a coalition to which 41 nations contribute.
Defense officials described him as a “straight shooter” largely expected to approach the war with a more realistic attitude of defeating the Taliban than General Nicholson, who on multiple occasions suggested that the United States had turned a corner in the war.
General Miller, who overlapped with General Nicholson as a cadet at West Point, is well regarded, but his 35 years of service have been spent mostly with the Special Operations community. That has left little time for larger and more public-facing commands that, by nature, are exposed to political nuances from which their commando counterparts are usually insulated.
At General Nicholson’s side at the ceremony on Sunday was his wife, Norine MacDonald, a security analyst and researcher who has long been active in Afghan affairs. The two met at an event on Afghanistan.
Ms. MacDonald — who has served as a “first lady” of sorts, her presence encouraging more female voices — accompanied her husband on trips to front-line provinces and high-level meetings, a strong statement in a country where decision-making is dominated by men.
But her prominent role in a war zone, where movement is so limited that officers take helicopter shuttles to travel even the smallest distance out of headquarters in Kabul, was disorienting to many soldiers who had seen nothing quite like it.
Ms. MacDonald’s years of work in Afghanistan, which she paused after General Nicholson took command, defied easy labels to those who saw her in action.
She distributed emergency food to families displaced by the “bombings and eradication campaigns” of the United States-led military coalition, wrote research papers and provided video reportage from difficult corners of the country, vocal against the “blowback” of operations pushing young men to the arms of the Taliban.
A strong theme of her work was grass-roots mobilization against the eradication of poppies, passionately arguing that Afghanistan could gain by legalizing the crop for medicinal purposes.
That infuriated Afghan and United States officials at the time when eradication was the American policy. WikiLeaks cables showed American and Afghan officials repeatedly discussing “efforts to rein” her in.
Ms. MacDonald’s offices were raided by Afghan intelligence, her equipment confiscated, and she was asked to leave the country. While she scrambled to find caretakers for her Russian jeep and motorcycle that she drove around Kabul, and the pet turtle she kept at her home, it was not clear whether she ever left.
“Your service truly is selfless. Thanks for your work in Afghanistan, thanks for putting your career on hold,” General Votel said of Ms. MacDonald at the farewell ceremony on Sunday before she, teary-eyed, walked arm in arm with General Nicholson to the helicopter that would usher them away.