CANNON BALL, N.D. >> The fires burned for hours on the flat, muddy landscape, their thick smoke rising through snowflakes that tumbled to the ground. Someone rode a snowmobile across the dirt, and others moved their belongings to the side of a rural highway. The police gathered, prepared to follow the governor’s order to clear people from this rural part of the state.

But the Wednesday afternoon deadline for protesters of the Dakota Access oil pipeline to empty their largest encampment passed with far more uncertainty than unrest. In the hours after the deadline, the authorities made 10 arrests but said they would not fully empty the camp on Wednesday night.

Roughly 25 to 50 demonstrators were believed to remain in the mandatory evacuation zone, said Gov. Doug Burgum, who said cleaning crews planned to enter the camp Thursday morning. “Anyone who obstructs our ability to do cleanup will be subject to arrest,” Mr. Burgum said.

The scene here, about an hour’s drive south of Bismarck, the state capital, seemed to represent a muffled end to a specific and passionate protest that drew thousands of demonstrators and became central to the national debate about energy, the environment and the rights of Native Americans. Protesters argued that the nearly completed pipeline, now moving ahead with the support of President Trump’s administration, could imperil the drinking water supply on the Standing Rock Sioux Reservation.

“We won,” said Vanessa Red Bull, 54, who has spent months here. “We slowed that pipeline down months and months and months. We cost them who knows how much money. And we slowed them down.”

She added, “This has been a multilayered event that has brought attention to glaring issues.”

Ms. Red Bull and her allies won a brief victory last year, when the Army Corps of Engineers said in the waning days of the Obama administration that it would conduct an environmental impact study before allowing the 1,172-mile pipeline to cross Lake Oahe, the Missouri River reservoir near the encampment. But the beginning of the Trump administration brought a swift and substantial defeat: an instruction that the Army abort its study, a decision that allowed construction to resume.

Barring court intervention, oil from the Bakken fields in western North Dakota could flow through the pipeline this spring. But on Wednesday, the matter at hand was what to do with the encampment, which had become an abiding and, for some, spiritual symbol of activism. State authorities cited fears of flooding for the governor’s decision last week to order a mandatory evacuation of the site.

“It’s time for protesters to either go home, or move to a legal site where they can peaceably continue their activities without risk of further harm to the environment,” the North Dakota attorney general, Wayne Stenehjem, said in a statement. Officials said that trash at the protest camps posed an ecological risk if it were washed downstream by flooding, and that urgent cleanup was necessary.

Both sides have accused the other of escalating tension and engaging in violence since the protest started last year as a decidedly local affair. The camps ultimately swelled to thousands in the summer and fall, with Native Americans and supporters from across the country gathering in spirited opposition and setting up a makeshift society in the camps, complete with cooking tents and supply areas.

But on Wednesday, months of tension mostly gave way to a somber calm as demonstrators left and a cold rain turned to snow. Some protesters set fire to semipermanent structures ahead of the 2 p.m. deadline.

“It’s an act of defiance,” Nick Cowan, 25, said as he watched a fire burn on Wednesday after living here for more than two months. “It’s saying: ‘If you are going to make us leave our home, you cannot take our space. We’ll burn it to the ground and let the earth take it back before you take it from us.’”

Two youths were injured at the camp Wednesday, apparently from the fires, officials said, including a teenage girl who was hospitalized with severe burns.

North Dakota officials offered meals, lodging, a medical exam and a bus ticket to anywhere in the 48 contiguous states for protesters who left by Wednesday afternoon but needed help getting home.

That approach was at odds with events of recent months, when the demonstrators sporadically clashed with the police, leading to the activation of the North Dakota National Guard and hundreds of arrests. The police sometimes used tear gas and rubber bullets. The North Dakota Guard said on Wednesday that it had spent more than $8 million responding to the protest since August.

Despite the lingering frustrations, tensions seemed to have eased in recent weeks as the ranks of demonstrators declined during the harsh winter. Dave Archambault II, the chairman of the Standing Rock Sioux Tribe, which has sued seeking to block the pipeline construction, urged protesters to go home.

On Wednesday, many of them did.

“I think people are saying goodbye,” said Ms. Red Bull, who spent about six months here. “I think that’s why people are setting things on fire as a way of a last homage to what had become many people’s homes. A community was here.”

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