It started with a duffel bag containing sex toys, cigars and a pornographic film.
The bag belonged to James Burke, the police chief in Suffolk County, and was stolen from his parked car in December 2012. When the police later arrested a heroin user with the bag, Mr. Burke walked into the station house to confront the man, who was handcuffed to the floor of an interrogation room.
For a few minutes, prosecutors said, Mr. Burke assaulted the suspect, screaming and threatening to kill him until a detective in the room finally said, “Boss, that’s enough.”
The assault prompted a federal criminal investigation that lasted more than four years and eventually led to the resignation not only of the police chief but also of the longtime Suffolk County district attorney, Thomas J. Spota, who was accused of trying to cover it up.
This week, Mr. Spota goes on trial along with one of his top deputies, Christopher McPartland, in a case that could expose the inner workings of a law enforcement culture on Long Island that has been plagued by longstanding accusations of corruption.
Opening statements are expected to begin on Thursday morning. Prosecutors will lay out their case that Mr. Spota and his deputy directed a cover-up to protect Mr. Burke, pressuring potential witnesses not to cooperate with the federal investigation into the assault. Several police officers are expected to be called as witnesses.
Mr. Spota and Mr. McPartland have pleaded not guilty to four criminal counts, including witness tampering and obstruction of justice. Their lawyers have said they are innocent, arguing among other things that Mr. Burke never admitted to them he had assaulted the man who was found with his bag.
The case is a rare instance in which a district attorney is the one on trial. Mr. Spota, 78, served for more than 15 years as the top prosecutor in Suffolk County, on the eastern end of Long Island. The county has one of the largest police forces in America and includes both working-class villages and wealthy enclaves like the Hamptons.
Mr. Spota was a longtime Republican who ran as a Democrat to win election in 2001. He fought aggressively to expose sexual abuse by Catholic priests and was widely praised for prosecuting corrupt officials in both parties. Mr. McPartland, 53, was the chief of the office’s public corruption unit.
Prosecutors, however, have said in court papers that Mr. Spota and Mr. McPartland “operated in a manner more akin to criminal enterprise than a district attorney’s office.”
Federal prosecutors have described a climate of fear and retribution cultivated by top law enforcement officials in Suffolk County, where subordinates worried their careers would be destroyed if they did not obey corrupt orders.
The local police department had long faced allegations of coerced confessions and abuses of power, and critics raised concerns about the cozy relationship between the police and local prosecutors.
Mr. Burke, the former police chief, once asked to install a surveillance device on another police official’s car because, according to the government, he disliked her and wanted to see whether he could dig up dirt that could be used to end her career.
“That’s something out of the K.G.B.,” a prosecutor said at Mr. Burke’s bail hearing in 2015.
Mr. Burke’s lawyer said at the time that the surveillance was part of a legitimate investigation into whether the officer had been filing false time sheets.
A few months after the 2012 assault, the man caught with the duffel bag, Christopher Loeb, told investigators that Mr. Burke had beaten him, prompting a federal civil rights investigation. (Mr. Loeb later received a $1.5 million settlement from the county and a separate confidential settlement from Mr. Burke.)
By the end of 2013, the investigation had stalled and no criminal charges had been filed because Mr. Spota, Mr. McPartland and others had pressured witnesses to lie under oath and to withhold information from investigators, prosecutors said.
But in 2015, the prosecutors, in the Eastern District of New York, started investigating again, issuing grand jury subpoenas to police officers.
When Mr. Spota heard the inquiry was resuming, he “went nuts,” according to a court filing from the F.B.I.
At one meeting in 2015, Mr. Spota said that any police officers who flipped were “dead” and “would never work in Suffolk County again,” the filing said. During the same meeting, Mr. Spota, Mr. McPartland and Mr. Burke discussed who was a “rat” and directed a police officer to remind other officers what happened to people who “go against the administration.”
Mr. Spota and Mr. McPartland are also accused of requiring police witnesses to hire people from a list of lawyers who were expected to share information with Mr. Burke’s legal team, prosecutors said.
Ultimately, Mr. Burke was arrested and pleaded guilty in 2016 to a civil rights violation and conspiracy to obstruct justice. He was released from prison this year after receiving a 46-month sentence.
Mr. Burke has not cooperated with prosecutors and is not expected to testify at the trial of his former colleagues.
Mr. Spota had been a longtime mentor and friend of Mr. Burke’s. Their relationship began four decades ago in an unusual way: As a teenager, Mr. Burke testified as a witness in a homicide trial in which Mr. Spota was the prosecutor. The case was notorious on Long Island. The victim was a 13-year-old boy who died when other teenagers shoved rocks down his throat.
Lawyers for Mr. Spota and Mr. McPartland have accused the government of using “overly aggressive tactics” during their investigation. During the trial, which is expected to last four weeks, current and former Suffolk County police officers are expected to appear as witnesses.
The defense will most likely seek to undermine their credibility, pointing out to jurors that some of them have pleaded guilty to obstruction and are cooperating with prosecutors in hopes of receiving reduced sentences.
In court papers, the defense has suggested that Mr. Burke never told Mr. McPartland or Mr. Spota that he had committed the assault. For the defense, one critical issue at the trial will be whether Mr. Burke openly admitted his guilt.
“This is a pivotal point because the government’s prosecution rests on the theory that both defendants knew that Burke was guilty of the assault and took steps to help him cover the assault up,” the lawyers, led by Alan M. Vinegrad and Larry H. Krantz, wrote.
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