John Collado was on his way to buy groceries one September afternoon in 2011 when he spotted a neighbor and a stranger fighting on his block and pulled them apart.

“Stop! Stop! Stop!” Mr. Collado shouted as he stood between them on Post Avenue in Upper Manhattan, a hand extended toward each man’s chest, according to court documents. But the stranger — who turned out to be an undercover narcotics detective — pulled out a gun. Without a word, he fatally shot Mr. Collado in the stomach.

The detective, James Connolly, later testified that he fired in self-defense after Mr. Collado placed him in a chokehold. But a civil jury determined last year that his claim was false, and on Thursday New York City agreed to pay $5.5 million to settle a federal lawsuit claiming the detective used excessive force that was brought by the unarmed man’s widow, Amarilis Collado.

“I want to clarify that in reality my husband tried to make a good action, not to hurt an officer,” she said in an interview. “He tried to help by breaking up a fight.”

The settlement comes as a police shooting last month in which plainclothes anti-crime officers accidentally killed their partner has focused attention on deadly encounters involving plainclothes and undercover officers.

While they are a small fraction of the New York Police Department, plainclothes officers make up between one-quarter and one-third of officers involved in adversarial shootings, according to recent police reports on officers’ use of force.

Less than one percent of the city’s officers ever fire their service weapons outside of training, and even fewer do so in confrontations with suspects.

Plainclothes officers typically belong to units with the mission of catching people with guns and drugs, work that often pits them against violent suspects. Confusion can arise when officers in street clothes make an arrest or draw their weapons, which happened in Mr. Collado’s case.

The settlement also comes as the city is grappling with five fatal police shootings in four weeks, and it highlights the difficulties faced by families when they try to hold officers responsible for what they believe are unjustified deaths.

In the eyes of the city and the Police Department, Detective Connolly’s actions were justified. He was later promoted to sergeant.

“We believe Sergeant Connolly was put into a terrible life or death situation and forced to make a harrowing choice,” said Nick Paolucci, a spokesman for the city’s Law Department, noting that the judge wrote in his decision on post-trial motions that the sergeant “did not act with evil motive or intent or reckless or callous indifference to Collado’s federally protected rights.”

“Nevertheless,” Mr. Paolucci added, “the parties have agreed that this settlement will end a longstanding and tragic case in their best interests and will bring a measure of closure to Mr. Collado’s family.”

It was not the first time Sergeant Connolly, a 35-year-old former Marine, had killed someone in the line of duty: While working undercover in 2009, he fatally shot a teenager who tried to rob him at gunpoint during a cocaine deal.

Two grand juries and a police firearms panel found no wrongdoing by Sergeant Connolly in either killing, although the civil jury in the Collado case found that medical evidence, surveillance video and witness testimony contradicted his account.

Judge Denny Chin is expected to approve the agreement filed on Thursday in federal court in Manhattan, almost a year after the civil jury determined that Sergeant Connolly had no reason to fear for his life when he shot Mr. Collado, 43. The verdict followed an earlier mistrial.

Sergeant Connolly declined to discuss the case on Thursday, citing a Police Department policy requiring him to seek approval first.

“This is all a judgment call and, unfortunately, public perception is that cops are the bad guys,” Edward D. Mullins, president of the Sergeants Benevolent Association, the union that represents Sergeant Connolly, said of the settlement. “And I hate to feel that this is impacting jury pools, but I’m not shocked.”

The day Mr. Collado died, Sergeant Connolly had left his partner behind to look for drug activity on his own. He testified that he saw Rangel Batista, a convicted drug dealer, sell marijuana to someone else inside a building on Post Avenue in the Inwood neighborhood.

Sergeant Connolly said he identified himself as an officer and tried to arrest Mr. Batista. They fought. Their struggle spilled outside onto the sidewalk and across the street, where Mr. Collado was headed to the supermarket to buy lasagna ingredients.

Sergeant Connolly and Mr. Batista had been fighting for about a minute and a half when Mr. Collado intervened. The sergeant testified that he was on the ground under Mr. Batista when Mr. Collado picked up Sergeant Connolly from behind, an account corroborated by a female witness. Then, he said, Mr. Collado placed him in a chokehold and lifted him off the ground.

The sergeant said on the stand that he was close to passing out when he fired a single round, an account the Police Department repeated in its 2011 report on firearms discharges.

At the civil trial, the woman was the only witness who said Mr. Collado had made contact with Sergeant Connolly’s neck, and she said the hold had lasted just a few seconds. Other witnesses said Sergeant Connolly was standing apart from Mr. Collado when he fired.

The civil jury awarded Mr. Collado’s estate $14.3 million, from which Judge Chin cut $10 million in punitive damages because he said he felt they were inappropriate. The judge said that without knowing Mr. Collado’s intentions, Sergeant Connolly “found himself in what objectively was a perilous situation.”

Rather than face an appeal from Mr. Collado’s widow, the city agreed to settle the lawsuit for $5.5 million, including $1.5 million for her lawyers.

It is rare for an officer to shoot and kill twice.

On Jan. 15, 2009, Sergeant Connolly shot and killed Anthony Roman, 18, during a botched cocaine purchase in Washington Heights. The sergeant said Mr. Roman had pulled a gun and tried to rob him after he complained that the young dealer had given him counterfeit drugs. The officer handed Mr. Roman cash with his left hand then shot him three times with a gun hidden in the right pocket of his jacket. Mr. Roman died six days later.

After Mr. Roman’s death, Sergeant Connolly was transferred from the 33rd Precinct in Washington Heights to the 34th Precinct, which covers the upper end of the neighborhood and Inwood just north of it.

The two precincts had been one until 1994, when the Police Department divided the 34th Precinct in part to get a handle on the drug violence that once made Washington Heights the city’s murder capital. They were among New York’s safest neighborhoods by the time Sergeant Connolly encountered Mr. Roman and Mr. Collado.

The city paid $50,000 in 2011 to settle two other lawsuits involving Sergeant Connolly, according to Capstat, a database of federal lawsuits filed against New York City police officers.

Mrs. Collado’s lawyer, Sam Shapiro, said the Collado case “is a prime example of the way in which the N.Y.P.D. and the city rally around their officers in the face of police violence” while painting unflattering portraits of the people killed as well as their families.

When he was killed, Mr. Collado was the primary caregiver for his mother, who has from Alzheimer’s disease, and his 2-year-old son, John J., the youngest of his six children. He had worked as a building superintendent and later in a hotel before resigning because of a spinal injury, his widow said.

Mrs. Collado has said that her husband supported and defended the Police Department, but that the police killed him and then, in her view, smeared his name. The department, she said, has never acknowledged that Mr. Collado was a good Samaritan who had done nothing wrong.

“A lot of people think that whenever one files this type of lawsuit we’re thinking about the money,” she said. “In this case, it was the only option that I had for people to recognize in some way the guilt of the police and the injustice that was done with my husband.”

Sheelagh McNeill contributed research.

Ashley Southall is a law enforcement reporter focused on crime and policing in New York City. @AshleyatTimes

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