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 plagued by longstanding accusations of corruption.