WASHINGTON — After the Sept. 11 attacks, Joseph Astarita sought to follow in the footsteps of his father, an F.B.I. agent, joining the bureau and later earning a spot on the New York office SWAT team.

But he dreamed of joining the elite Hostage Rescue Team, and after a failed effort, he landed with the unit on his second try in April 2015.

Now Mr. Astarita faces prison, the ultimate disgrace for an agent sworn to uphold the law. He was indicted on charges of lying and obstruction of justice after a deadly clash with a well-known anti-government activist. His federal trial starts Tuesday in Portland, Ore., and is expected to last several weeks, putting a spotlight on the F.B.I.’s Hostage Rescue Team.

Prosecutors say Mr. Astarita, 41, tried to cover up the firing of two shots during the arrest of the activist, LaVoy Finicum, during the confrontation at a remote federal wildlife refuge in January 2016 in Oregon.

Mr. Finicum was part of a small group of armed militants who had been protesting at the Malheur National Wildlife Refuge near Burns, Ore. Led by two brothers from a Nevada ranching family, Ammon and Ryan Bundy, they were protesting the imprisonment of a pair of ranchers convicted of lighting fires that burned federal land.

Video footage recorded by a passenger in Mr. Finicum’s truck showed that the shots were fired after he stepped out. Prosecutors believe only Mr. Astarita could have fired those shots, basing their case on surveillance videos and photographs.

Mr. Astarita has maintained his innocence, and many of his hostage rescue teammates believe him. His lawyers, who declined to comment, recently wrote in court documents that Mr. Astarita had training that helped keep him from firing the shots, a point they are likely to emphasize at trial.

“He is one of the nation’s most elite, well-trained and disciplined shooters,” they wrote. “He would not have fired in these circumstances. And if he had, he would not have missed.”

But why would Mr. Astarita lie about the shooting? Prosecutors have a theory: Because agents are prohibited from firing into vehicles except under certain circumstances, admitting he shot at Mr. Finicum might have cost Mr. Astarita his coveted spot on the hostage rescue unit.

The trial comes at a difficult time for the F.B.I., which has been repeatedly maligned by President Trump for investigating whether any of his associates colluded with Russia to interfere in the 2016 election. A conviction would be a black eye for the bureau and in particular the hostage team, which has been involved in some of the country’s most sensitive counterterrorism operations.

The F.B.I. director, Christopher A. Wray, praised the hostage team during an appearance last month before Congress, noting it had recently carried out more than two dozen missions. Created in 1983, the rescue team also has worked closely overseas with American military commandos.

This month, the judge dismissed two of the charges against Mr. Astarita, handing his defense a partial victory. But the judge also refused to allow defense lawyers to question an Oregon State Police trooper at the scene about who fired the shots. He thought one of his fellow troopers fired into Mr. Finicum’s truck but did not witness it. The judge said the trooper could testify only about what he saw.

Little evidence ties Mr. Astarita to the shooting. Authorities never found the bullets or the casings, and neither the troopers nor the agents saw Mr. Astarita discharge his gun. Grainy surveillance footage taken from an F.B.I. plane shows agents milling around after the shooting. One can be seen bending over and possibly picking up something.

The case essentially boils down to a computer model that points to Mr. Astarita as the possible shooter based on the trajectory of the bullets. Mr. Astarita’s lawyers call the model flawed, saying it is impossible to determine his exact position during the shooting.

They also believe that a state trooper standing near Mr. Astarita was most likely responsible.

During the confrontation, a pair of troopers fired a total of six shots. One shot three times into Mr. Finicum’s truck as it barreled down the road before crashing into a snowbank. Both troopers then opened fire on Mr. Finicum, 54, as he exited the truck, hitting him three times.

The trooper who fired at the truck, a veteran of the Oregon State Police and now a captain, was involved in at least three other shootings and cleared in all of them. Defense lawyers are expected to question the captain, but he will not be identified by name during the trial because of threats made on his life, the judge said.

The shooting of Mr. Finicum was one of the more dramatic episodes of a 2016 standoff between federal officers and the anti-government ranchers and militiamen who had taken over the wildlife refuge.

This month, Mr. Trump pardoned the imprisoned ranchers, Dwight L. and Steven D. Hammond, and they flew home on a private jet owned by an oil products executive who had lobbied for their release.

The 2016 occupation quickly morphed into a broad protest for anyone angered by perceived federal overreach, and Mr. Finicum became one of the most recognizable faces of the occupation.

An Arizona rancher with 11 children, he had his own conflicts with the federal government, and he roamed the refuge’s many buildings with a broad cowboy hat and a pistol on his hip.

At the time, sitting in the basement of one of the refuge buildings, he told a New York Times reporter that he was sure the takeover would not end with his imprisonment. “I would rather die than be caged,” he said.

Days later, Mr. Finicum and several of his allies took a car from the refuge to a neighboring community where they planned to spread their message of protest. But state and federal officials blocked the route, and Mr. Finicum leapt out of the car and began to run.

Official video released later showed him reaching toward his chest as he was shot. The authorities contend that they believed he was reaching for a loaded weapon inside his jacket while Mr. Finicum’s supporters say he was surrendering.