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The four remaining occupiers at an Oregon wildlife refuge surrendered Thursday morning after hours of tense negotiations, bringing an end to the weeks-long protest over land rights and personal liberties.

Federal officials said Jeff Banta, Sean Anderson, Sandy Anderson and David Fry were taken in without incident after FBI agents surrounded Malheur National Wildlife Refuge, about 300 miles southeast of Portland.

The FBI's decision to encircle the last of the holdouts marked a dramatic escalation to a mostly plodding armed demonstration at the isolated sanctuary, which began Jan. 2 as many out-of-state protesters descended on the property.

All four of those arrested Thursday are expected to face an arraignment before a magistrate judge in Portland on Friday.

In total, 25 people — including the holdouts — have been indicted on a charge of conspiracy to interfere with federal workers. The ringleaders, Ammon and Ryan Bundy, and other protesters were arrested last month, and Ammon Bundy through his attorney called for the remaining occupiers to give up.

Greg Bretzing, the FBI's special agent-in-charge for Oregon, reassured supporters of the occupiers who simply visited the refuge or sent food that they won't be prosecuted.

"We are concerned about those who have criminal, violent intent," Bretzing said at a news conference Thursday afternoon.

Meanwhile, the refuge will likely remain closed "for several weeks" as authorities continue to investigate, he said, adding: "While the occupation is over, there is still quite a bit of work to be done."

People wave U.S. flags Thursday near Malheur National Wildlife Refuge near Burns, Oregon. Rebecca Boone / AP

Investigators were spending Thursday searching the buildings and the surrounding land to ensure that nobody remained, he said, and then the scene will undergo "tactical clearing" by local, state and federal bomb technicians.

It will then take "several months" to analyze all of the evidence, he said.

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Bretzing said authorities would be especially sensitive in handling "ancestral lands and artifacts dating back thousands of years," a concern that he said had been raised by members of the Burns Paiute Indian tribe.

"As we have said since day one, our goal has been to end this illegal occupation peacefully, and we are grateful that we were able to do so today," he said.

Agents "moved to contain" the holdouts Wednesday after one of them allegedly drove outside previously established barricades and then back in at high speed when approached by the FBI, the bureau said.

RELATED: Meet the Colorful Lawmaker Allied With Oregon Occupiers

The occupation came to an emotionally heated conclusion as Fry, the last to leave, ranted about politics and threatened suicide in a live-streamed conversation with self-described "liberty activist" Gavin Seim and conservative radio host KrisAnne Hall.

Related: Who Are the Four Holdouts in the Oregon Refuge?

"I'm not coming out of here alive," Fry, 27, could be heard saying at one point. "I'll kill myself before you guys [expletive] do it."

Fry, of Blanchester, Ohio, said he was unhappy that his taxes were going toward abortions, drone strikes in the Middle East and the Affordable Care Act health insurance program.

"You have a very powerful voice. You have a very powerful passion," Hall could be heard saying, telling Fry that he would have more influence on the outside.

He walked out amid shouts of "hallelujah."

Nevada lawmaker Michele Fiore and evangelist Franklin Graham, two allies of the occupiers, were also outside as Fry surrendered about 11 a.m. (2 p.m. ET).

About an hour earlier, husband and wife Sean and Sandra Anderson, of Riggins, Idaho, and Banta, of Yerington, Nevada, agreed to walk out one by one. They said they would be unarmed and carrying an American flag.

Cliven Bundy, the father of Ammon Bundy, the arrested leader of the armed occupation of the Malheur National Wildlife Refuge, was booked in Multnomah County Jail Wednesday night. Multnomah County Sheriff

As the confrontation unfolded in Oregon on Wednesday, the Bundys' father, Cliven, 74, was taken into federal custody at the Portland airport. He was charged with assault and conspiracy in connection with a 2014 standoff near his Nevada ranch, according to a criminal complaint.

Bundy had an initial court appearance Thursday and is scheduled for a bond hearing Tuesday. Bretzing declined to say why the 2014 case was only now being prosecuted.

Thursday's events followed a phone call Wednesday night among the protesters and negotiators that was also live-streamed online. In the call, the occupiers warned that the incident could end in bloodshed.

Related: Federal Jury Indicts Arrested Oregon Protesters

The protesters who overran the refuge said they were standing up against the federal government. They demanded the return of federal land they felt had been taken from the public and the exoneration of two ranchers convicted of setting fires that spread to public land.

Ryan and Ammon Bundy, ages 43 and 40, were among five occupiers arrested during a traffic stop on Jan. 26 as they drove to a public meeting.

Another vocal member of the group, Robert LaVoy Finicum, 54, was shot dead during that encounter with law enforcement officials who said he ignored their demands to surrender. Finicum's family rejects the FBI's suggestion that he was armed.

Federal prosecutors, meanwhile, unsealed an indictment Thursday in Portland charging nine more of the occupiers with the same interference count as the 16 people previously announced.

The indictment provides few details, but it alleges that all nine were at the refuge until the mass surrender on Jan. 26. Seven of the nine are in custody and were identified as:

Blaine Cooper, 36, of Humboldt, Arizona

Wesley Kjar, 32, of Utah

Corey Lequieu, 44, of Fallon, Nevada

Neil Wampler, 68, of Los Osos, California

Jason Charles Blomgren, 41, of Murphy, North Carolina

Darryl William Thorn, 31, of Marysville, Washington

Eric Lee Flores, 22, of Washington

The names of the two others are redacted in the indictment because they're still at large.