In June, as security worsened in Afghanistan, National Security Adviser Jake Sullivan began to raise questions about the rapid pace of U.S. military withdrawal.

The Pentagon was planning to pull out the bulk of its force and shut Bagram air base by early July to minimize the risk to its troops. With a large U.S. Embassy staff in Kabul and fresh intelligence suggesting the Afghan government was weakening, Mr. Sullivan, whose duties are to coordinate policy, questioned whether it was prudent to close the base so soon, according to U.S. officials.

As the process of closing Bagram neared the point of no return, the military paused the shutdown on June 18 so the White House could ponder the ramifications of giving up the U.S.’s premier air base in the country. On June 22, President Biden signed off on the plan to close the base on July 2 and keep only a limited military presence on the ground.

The decision helped propel the U.S. down a path toward what became a tumultuous ending to the 20-year war that will leave a mark on Mr. Biden’s presidency. The Taliban quickly overran the Kabul government, the U.S. left the majority of Afghans at risk behind, and people around the world watched televised scenes of airport chaos. An Islamic State group suicide bomber killed at least 180 people crammed around Kabul’s airport, including 13 American service members, according to Afghan and U.S. officials.

A consequence of the Biden administration’s push to quickly draw down the military was to keep the Defense and State departments on divergent paths. The accelerated military exit contrasted with the State Department mission of maintaining a robust embassy and full-scale diplomatic support for Kabul well after American forces left.

That reflected the administration’s assumptions and initial intelligence estimates that the Afghan government could hold off the Taliban for as long as two years after U.S. troops were gone. The strategy became untenable as the Taliban swept across the country and the Afghan government and military crumbled.

While many factors, recent and long past, contributed to America’s drive to leave Afghanistan, among the problems, interviews with a wide range of officials suggest, was the difficulty the Biden administration had in quickly adjusting to changing circumstances as the Taliban advanced, as more-pessimistic intelligence assessments arrived and as military officials raised alarms that Washington was moving too slowly to help Afghan allies.

Ending U.S. military involvement in Afghanistan had long been an overriding objective for Mr. Biden and something he campaigned on. After he announced in April that the last 2,500 or so U.S. troops would leave by Sept. 11, the military leadership, although recommending keeping those troops there longer, fell in line. Top civilian aides maintained hope, fortified by optimistic intelligence assessments about how long the Afghan government could hold out against the Taliban.

In the final weeks, the administration switched course and reinserted thousands of troops, to conduct a hurried evacuation of civilians. While the effort it undertook with its allies got more than 124,000 civilians out, it left behind as many as 200 American citizens and the majority of tens of thousands of Afghans who had worked for the U.S. or its NATO allies.

Administration officials vow to help Americans and former Afghan allies who want to get out of Afghanistan to leave the country, without providing details, emphasizing that the effort would rely on economic leverage and diplomatic means.

Afghans trying to flee clamored to show their credentials to authorities at the Kabul airport on Aug. 26.

Photo: akhter gulfam/EPA/Shutterstock

Overseeing the steady glide to withdrawal was a president with decades of foreign-affairs expertise and a tight circle of advisers who included Defense Secretary Lloyd Austin, a retired general who oversaw the U.S. troop withdrawal from Iraq, and on the civilian side Mr. Sullivan and Secretary of State Antony Blinken —two men with long experience in policy-making but little in managing war-zone crises.

The National Security Council “and the upper echelons of government are neither trained or constituted to execute complex operations. Their job is to set and monitor policy,” said Ronald Neumann, a former U.S. ambassador to Afghanistan who is president of the Academy of Diplomacy, an association of ex-ambassadors. “In this case, understanding execution was essential for making realistic decisions, and they fell well short of their own goals.”

Defending his administration’s handling of the withdrawal, Mr. Biden said this past week that his national-security team planned for “every eventuality” and that the end of the U.S. military presence was bound to be chaotic whenever it occurred. “There is no evacuation from the end of a war that you can run without the kinds of complexities, challenges and threats we faced,” Mr. Biden said on Tuesday.

Mr. Sullivan declined through a spokesman to discuss his role in internal deliberations. Mr. Austin, when asked by reporters, said the U.S. government’s slow process for dealing with Afghans eligible for special immigrant visas compounded the problems. He declined to pinpoint any Pentagon mistakes, saying this would be the subject of after-action reviews.

“No operation is ever perfect....We want to make sure that we learn every lesson that can be learned from this experience,” Mr. Austin said.

A spokesman for Mr. Blinken had no comment. A State Department official defended the administration’s performance given, he said, the unprecedented circumstances.

“If there was an expectation that this team could prevent crises, that’s not how it works,” the official said. “People will question certain decisions, but the fact is no one has been confronted by a situation like this.”

Bagram Airbase in Afghanistan in July after the American military left.

Photo: Paula Bronstein for The Wall Street Journal

Mr. Biden entered office in January with the clock ticking toward a May 1 U.S. withdrawal deadline, a date agreed on by the Trump administration and the Taliban in talks last year. As vice president, Mr. Biden had advised then-President Barack Obama that Afghanistan was a quagmire and that the military would try to narrow his options.

Though Mr. Biden reversed other Trump policies, he was inclined to go through with the Afghan agreement, while extending its withdrawal date about four months. The alternative, he has since said, would be inflaming relations with the Taliban and more fighting, with U.S. troops at risk.

The military argued for keeping 2,500 troops in the country, the stated size of the force at the time, although the actual number ranged toward 3,500 when classified and some other units were included, according to U.S. military officials. Bagram air base was central to the military’s plans because it would provide a staging area for drones, other aircraft and special-operations forces to conduct counterterrorism operations in case terrorist and other dangers grew.

Before Mr. Biden’s April announcement, military officials sensed that he wanted to bring the military role in Afghanistan to an end. When Mr. Austin traveled to Afghanistan in March, the top U.S. commander there, Gen. Scott Miller, told him he could get all American forces out in two months if he had to, according to U.S. officials.

While first setting a withdrawal deadline of the 20th anniversary of the Sept. 11 terrorist attacks that precipitated the war, Mr. Biden later cited the swiftness of the Pentagon’s drawdown in advancing the date to Aug. 31.

The day after the president’s April 14 announcement, Mr. Blinken visited Kabul and committed to providing the country with a full “diplomatic, economic, and humanitarian toolkit to support the future the Afghan people want, including the gains made by Afghan women,” including after American forces left.

Securing the embassy, with some 4,000 American, foreign and Afghan staff, during the drawdown became an immediate priority. State and Defense officials settled on a plan to retain 650 troops to guard the embassy and secure Hamid Karzai International Airport, and the White House approved, officials said. Following the decision, the embassy ordered nonessential staff to leave Afghanistan, in what would become the first of several rounds of reductions.

Secretary of State Antony Blinken, right, in April with Afghan Foreign Minister Mohammad Hanif Atmar outside the presidential palace in Kabul.

Photo: Afghan presidential palace/Shutterstock

On May 8, the Pentagon hosted a meeting in its basement auditorium to be sure that it, the National Security Council, the State Department and other parts of the administration were aligned on winding down the U.S. role. Chief among the topics, officials said, was conveying the military’s plan for rapid withdrawal to minimize the risk to troops.

Mr. Austin and Joint Chiefs of Staff Chairman Gen. Mark Milley told the group—which included Mr. Sullivan and Deputy Secretary of State for management Brian McKeon, who was overseeing the U.S. Embassy in Kabul—that the military would be out by the first week in July, except for the 650 troops guarding the embassy and airport. A PowerPoint presentation on the withdrawal included the planned closing of Bagram air base, nearly 40 miles north of Kabul, and Camp Dwyer, an air base in Helmand province.

“We realized the need to bring everyone in physically and communicate this,” said a defense official.

The Pentagon wanted a discussion on an emergency evacuation of the embassy and how to plan to remove Afghans at risk, but White House officials asked that those issues be removed from the agenda, saying they should be discussed separately, according to U.S. officials.

Within the administration and the U.S.-led coalition, worries rose. In policy coordination meetings, Samantha Power, head of the U.S. Agency for International Development, raised mounting concerns that Afghan groups that carried out her agencies’ aid programs could be caught in the crossfire, officials said.

A new intelligence assessment, prepared in mid-June at the request of Gen. Milley, said Kabul could fall six months after the U.S. military left.

That was when Mr. Sullivan at the NSC raised questions about shutting down Bagram, according to U.S. officials. With only two weeks before most of the military was due to leave, the base was in the process of being closed. The Pentagon, which was also cognizant of the significance of the impending move, paused the shutdown for several days so Mr. Biden and his aides could reconsider the timing of closing the base. Keeping it open would delay the Pentagon in carrying out Mr. Biden’s plan to remove the vast majority of American troops.

Working with the administration’s troop limit of 650, military commanders had to choose between keeping open Bagram or the Kabul airport, which was thought ready to handle a large evacuation. Briefed about it, U.S. officials said, Mr. Biden backed the military plan, affirming Bagram’s closing.

“Securing Bagram is a significant level of military effort of forces, and it would also require external support from the Afghan Security Forces,” Gen. Milley said at a Pentagon press conference last month. “Our task was protect the embassy in order for the embassy personnel to continue to function.”

“So we had to collapse one or the other, and a decision was made,” Gen. Milley added. Operating out of the Kabul airport, he said, “was estimated to be the better tactical solution in accordance with the mission set we were given and in accordance to getting the troops down to about 600, 700 number.”

Gen. Scott Miller, center, the former top U.S. commander in Afghanistan, with Joint Chiefs of Staff Chairman Gen. Mark Milley, right, and Secretary of Defense Lloyd Austin, left.

Photo: Alex Brandon//Press Pool

The military in Kabul for weeks pushed American diplomats there to shrink the size of the embassy to reduce the exposure to danger if the capital fell to the Taliban, fearing that the thousands of people still living and working in the complex would be hard to protect or evacuate in a crisis, officials said. State officials were reluctant to do so, according to U.S. officials.

Embassy officials were already overseeing some reductions, another official said. Over the course of July, the embassy sent home an additional 400 Americans, according to this official.

A day after Gen. Miller’s departure, two dozen U.S. Embassy officials decided they would no longer be silent about what they saw as a rapidly deteriorating situation. A classified dissent cable, dated July 13, to Mr. Blinken and another State Department official warned of an imminent Taliban takeover and a need to begin mass evacuations of Americans and their Afghan partners as soon as Aug. 1. On Aug. 3, days before the first provincial capital fell to the Taliban, a new U.S. intelligence assessment concluded Kabul could fall within months or even weeks, officials said.

“By then, everything was blinking red,” said a U.S. official familiar with the cable. “It takes a lot for folks to go around leadership.”

With the Afghan forces faltering, the Biden administration resumed manned airstrikes, which had been curtailed with the closure of Bagram, by flying from bases in Arab Gulf states. To do so, the U.S. secretly sent a team to the Kabul airport that could carry out search-and-rescue missions if an American aircraft ran into maintenance problems and crashed, a military official said.

The State Department also looked to speed up the process of getting Afghan allies out of the country. The 14-step process of issuing these special immigrant visas took two years on average.

The program had seen multiple disruptions over the past year when Covid-19 outbreaks forced the embassy to suspend the service and eventually to relocate application processing to Washington. Only 750 out of more than 20,000 pending applications were in the final stage.

The administration announced a new effort to support the relocation of interested and eligible Afghan nationals and their immediate families. A 24-hour task force was set up in Washington on July 19 to step in, and the first group landed in the U.S. on Aug. 1.

Ross Wilson was the acting U.S. ambassador to Afghanistan in the last days of the U.S. military presence.

Photo: wakil kohsar/Agence France-Presse/Getty Images

The State Department then broadened the pool of Afghans potentially eligible for resettlement in the U.S., announcing a new visa designation for any Afghan who had worked for U.S. government contractors, U.S.-funded programs or media organizations. The expanded effort raised expectations, contributing to the crush of Afghans who would later descend on the Kabul airport.

A senior State Department official said that the program’s lengthy processing is due to constraints imposed by Congress and couldn’t be cut. The decision to bring applicants to the U.S. or third countries before completing it, he said, required weeks of planning and approval from the president.

But those plans were crafted, the official said, when intelligence assessments suggested the U.S. still had more time to get allies out before Kabul risked falling to the Taliban.

On Aug. 6—the day the Taliban captured the first provincial capital at the start of a lightning, 10-day sweep that would bring them into Kabul—senior administration officials gathered to discuss the situation, focusing on whether to undertake an emergency evacuation of the embassy. Military officials urged coordination and emphasized to the others that the longer the U.S. waited to begin evacuating the embassy, the riskier it would become.

The embassy drew up plans to further reduce its size, officials said, and more staff left.

A Chinook helicopter flying over the U.S. embassy in Kabul in mid-August.

Photo: Rahmat Gul/Associated Press

With the Taliban making rapid advances, the Pentagon began to send troops back to Afghanistan to evacuate the embassy and Afghan allies. All told, it moved 5,000 troops back, about twice as many as were initially taken out. They were positioned at the Kabul airport and prompted the U.S. to turn to the Taliban, its longtime adversary, for help with security arrangements.

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In Doha, Qatar, U.S. envoy Zalmay Khalilzad negotiated a deal with the Taliban to remain on the outskirts of Kabul for two weeks while the U.S. completed its military withdrawal, officials said. During that period, a delegation of Afghan officials and power brokers was set to travel to Qatar to negotiate the handover of power to an interim government.

That never happened. Ashraf Ghani, the president of the U.S.-backed government, fled, and the Taliban entered Kabul on Aug. 15. The Taliban said they needed to take control of the city to prevent it from descending into chaos after the government fled. U.S. troops relied on the Taliban to maintain security on the outer edge of the airport while Afghans, Americans and others swarmed in to be evacuated.

Write to Michael R. Gordon at michael.gordon@wsj.com, Gordon Lubold at Gordon.Lubold@wsj.com, Vivian Salama at vivian.salama@wsj.com and Jessica Donati at jessica.donati@wsj.com