When night came, after long hours in the desert, the Afghan troops poured into a one-story schoolhouse and sprawled out on the floor. Outside, the Americans were crammed in mine-resistant vehicles, gauging the risks of sleeping next to their partners.

“All it takes is one bad guy. That’s all I’m saying,” said one soldier during the mission last month in eastern Afghanistan’s Paktika province. “I’m not crazy enough to sleep in there.”

Two weeks earlier, Staff Sgt. William “Billy” Wilson III had been shot and killed by a rogue Afghan police officer. That incident prompted some men in his battalion to question whether the U.S.-Afghan partnership in their corner of the country might soon give out. Some of Wilson’s friends secretly hoped it would.

But U.S. commanders went out of their way to assure American and Afghan soldiers that the partnership would not — could not — waiver, despite 20 incidents of fratricide this year. They mourned Wilson. They lectured their men on the Taliban’s efforts to weaken the alliance. And they planned a joint mission to Spina that would affirm their commitment and trust in the wake of tragedy.

“We tell them, ‘This is how the enemy tries to drive a wedge between us,’ ” said Capt. Jim Perkins, Wilson’s former commander. “We can’t let them succeed.”

The “shock absorbency” of the U.S.-Afghan relationship, some American officials say, has also kept Afghan soldiers from abandoning the partnership after NATO personnel burned dozens of Korans on a military base, and after Staff Sgt. Robert Bales was charged with murdering 17 civilians in Kandahar province. The relationship in the field appears to have reached a stasis in which isolated betrayals don’t threaten to undermine broader progress, they say.

That relationship has in Paktika become a transactional one, with Afghan forces dealing directly with Afghan villagers and Americans handling the operational logistics and much of the intelligence gathering.

Spina is considered one of the most significant Taliban strongholds in the region — a common stopover for insurgents on their way to and from Pakistan. There is no regular U.S. or Afghan security presence in the village. It’s so unstable that even the district sub-governor — Spina’s ostensible conduit to the capital, Kabul — hasn’t visited in five years. He lives nearly 10 miles away.

A ground mission would force Afghan and American soldiers closer together — on the same patrols and into the same makeshift bases. Col. Curtis Taylor announced the mission days before Wilson was buried, before writing a eulogy that included a line reflecting the blow endured by the 172nd Brigade: “His death hit this task force like a hurricane.”

Taylor was adamant that the storm not consume his battalion’s primary goal of extending the reach of the Afghan security forces. He said the mission would be “Afghan-led” — a term that U.S. military officials use to suggest the long-term sustainability of the decade-long war effort, which will soon be inherited by this country’s soldiers and policemen.

But to some of the U.S. battalion’s soldiers, that meant putting their lives in the hands of men whom they couldn’t trust. Wilson’s death was fresh when they packed in their armored vehicles last month and followed the Afghan army through the winding mountain passes that give way to Spina.

“You have to trust the Afghans, but you also have to protect your men,” Perkins said. “There is a residual concern to watch your back after these incidents.”

There was also some confusion about what “Afghan-led” really meant.

“How many of my men do you need?” asked Col. Safai Mirwais, head of the Afghan battalion partnered with Taylor’s.

“It’s your mission,” Taylor responded. “You tell me how many of my men you need.”

Taylor looks the part of the quintessential American soldier: broad-shouldered and impeccably uniformed. Mirwais traipses up the mountains of Paktika with a round belly and tattered black dress shoes.

When the military vehicles rumbled into Spina, Afghans and Americans were synchronized but separate. The Americans handed over intelligence reports to Afghan soldiers, who searched the homes of suspected insurgents. The Americans kept watch from hilltops as Afghans interrogated their suspects. The Americans listened to Taliban radio communications as the Afghans rushed toward buildings where the targets might be hiding. All the while, an American helicopter hovered overhead.

U.S. soldiers were unaccustomed to their role in the mission, which, at times, seemed peripheral.

“It’s sort of boring. The Afghans are doing what we normally do,” Staff Sgt. Joshua LeBel said.

Bored American soldiers watching Afghans carry out the critical duties of a mission is, in many ways, a sign of progress. But it remains far from the end goal: an autonomous Afghan force and a near-complete U.S. withdrawal. Afghans struggle with basic logistics and intelligence gathering. Those tasks will require more training and, above all, a continued Western presence. But in obscure villages such as Spina, those resources are unlikely to exist for long.

In the past, the United States might man an outpost or base for years before handing it to the Afghans. Now there’s no time for extended transitions; the plan is to build a checkpoint in Spina that will be immediately and exclusively manned by Afghans.

During the mission, when Americans received information about a Taliban fighter fleeing Spina on a motorcycle, Afghan and American troops gave chase — the Americans in mine-resistant vehicles and the Afghans in Humvees and pickups. When the mountain roads became too narrow, the soldiers continued the pursuit on foot, with the Afghans sprinting in one direction and the Americans in another.

The Americans settled into a position near a hilltop overwatch, where they intercepted a Taliban radio exchange: “They’re in our sights, and we are ready to shoot,” one insurgent said.

The American solders got down on their chests, waiting to be fired upon. The Afghans continued searching the dozen or so mud-baked huts that compose the village. It was unclear from the radio chatter which soldiers were being targeted; soldiers from both forces were warned.

“We’re about to get shot at,” one American said.

But a half-hour passed with no gunshots. Both forces started the walk back to the makeshift base. Some soldiers were disappointed that the mission had ended without direct exchange of fire with the Taliban. They knew that when the troops left the following day, insurgents would be back. Without a permanent presence in Spina, there was no way to root out insurgents.

That presence might be only months away. But it will require another joint operation — the first trip to Spina was crafted as strictly a scouting mission.

“Where you lead,” Taylor told Mirwais toward the end of the mission, “I’ll follow.”