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Sean Ellis in court.
Sean Ellis in court.Associated Press/File 1995/Associated Press

A Suffolk Superior Court judge has delivered a stinging rebuke to the leaders of Boston’s law enforcement community who oversaw the 1993 murder investigation of Detective John J. Mulligan, ruling the investigation was tainted by corrupt detectives and marred by prosecutorial failures.

In a 67-page decision on Tuesday, Judge Carol S. Ball ordered a new trial for Sean Ellis, 40, who was convicted in 1995 after two mistrials of first-degree murder for the Sept. 26, 1993 shooting of Mulligan, stating that the prosecution was in a “rush to judgment.” Ellis is serving a sentence of life without the possibility of parole.

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But Ball concluded that in the conviction of Ellis, “justice may not have been done’’ and said defense attorney Rosemary Scapicchio has unearthed new evidence that “suggests there was corruption within the investigation of Mulligan’s homicide itself.’’

In 2000, Ellis’s co-defendant, Terry Patterson, who was convicted in a separate trial as the person who shot Mulligan, had his conviction vacated and the fingerprint evidence linking him to the crime was discredited. Patterson eventually pleaded guilty to manslaughter and was released from prison in 2007.

Boston police referred a request for comment on Ellis’s new trial to Suffolk District Attorney Daniel F. Conley. A spokesman for Conley, whose office inherited the case from a predecessor and also argued against Ellis getting a new trial, disputed Ball’s findings, saying there’s “not one single piece of evidence mentioned in this decision” that “contradicts the strong evidence that proved Ellis’ guilt at trial.”

“In our judgment, this was a conviction based on direct, reliable, corroborated evidence. We fully intend to present that evidence to a new jury if necessary,” spokesman Jake Wark said in an e-mail.

Richard Mulligan, the slain detective’s brother who attended some of the hearings that led to Ball’s ruling, was disappointed by the judge’s decision.

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“Sean Ellis is guilty,’’ said Mulligan. “The evidence is compelling. I don’t think he’s fully paid for what he did.’’

While Ball’s ruling cited tips to police that Mulligan was involved in crimes with the detectives who investigated his murder, Richard Mulligan said his brother was never charged with anything and that the defense only seized on the issue to shift focus away from Ellis at a time when society is turning against police officers. He also noted that after his brother’s killing, three people close to Ellis were murdered.

“Death follows Sean Ellis,’’ Mulligan said.

Scapicchio said Tuesday that she plans to seek bail for Ellis, insisting that he is incarcerated “for a crime that he didn’t commit.”

In her ruling, Ball wrote that the top commanders of the Boston police should have been aware that Mulligan and three other detectives had been accused of participating in the armed robbery of a suspected drug dealer 17 days before Mulligan was killed.

Despite that knowledge, the three detectives, Walter F. Robinson Jr., Kenneth Acerra, and John F. Brazil, had key roles in locating prosecution witnesses or physical evidence used to convict Ellis. He was convicted of being involved in the murder of Mulligan, who was shot five times in the face with a .25-caliber handgun while he slept outside a Roslindale drug store on a paid detail, Ball wrote.

“From the beginning of the investigation, the apparent criminal misconduct of Detectives Acerra, Robinson, Brazil, and Mulligan gave the surviving partners a motive to cover up any evidence of their own crimes and to contribute to a quick arrest and conclusion to the investigation so that it did not turn in their direction,’’ Ball wrote. “Defense counsel should have had the opportunity to make that argument to the jury.’’

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Acerra, Robinson, and Brazil all pleaded guilty in US District Court in Boston in 1999 to corruption charges. Called this year as witnesses in Ellis’s motion for a new trial, all three men invoked their Fifth Amendment rights against self-incrimination and refused to testify.

“The newly unearthed evidence of the bias of Detectives Acerra, Robinson, and Brazil, who played significant roles in the homicide investigation, demands that a new trial be ordered here,’’ Ball wrote.

Ball also found that two former Boston police commissioners, William Bratton and Paul F. Evans Jr., should have known about the robbery of the suspected drug dealer under the department's own rules that required them to be notified of “significant’’ corruption allegations.

The information should have been shared with the defense before the first trial and also in 1996, when then-Commissioner Evans reopened an internal corruption probe that ended with the convictions of the three detectives, Ball wrote.

Bratton is now commissioner of the New York Police Department and could not be reached for comment Wednesday.

In a telephone interview Wednesday, Evans said he could not recall specific details of the investigation, but said that standard practice in the department was to turn over “anything and everything” that could be exculpatory to the defense.

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“I know I never intentionally withheld anything and I don’t think any of the people I worked with withheld anything,” said Evans. “I’m confident that we did what we were supposed to do.”

In 1993, Evans was the department’s superintendent-in-chief, and though he may have sat in on periodic briefings regarding the investigation, he was not a member of the task force investigating the murder. He said he was confident that police put the right man in prison.

“I feel bad for the Mulligan family, they’re going to be put through this,” he said.

Evans is the brother of current police commissioner, William B. Evans.

Ball also wrote that Phyllis Broker, who was then chief of former district attorney Ralph C. Martin 2d’s homicide unit, testified recently that she decided against investigating the connections between the detectives because “it didn’t affect me.’’

The ruling also noted, however, that Broker tried to remove Acerra from the task force after accusing him of planting evidence, and accused him and Robinson of misconduct handling a witness. Ball credited Broker with being the only person at the top echelon of police and prosecution overseeing the Mulligan murder investigation to try to ban the corrupt detectives.

In her ruling, Ball wrote that after Mulligan’s murder, Boston police received tips from three different individuals implicating a Boston officer and his son in the slaying. The tipsters said that the father and son believed Mulligan had allegedly harassed a teenaged female relative.

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Ball said the defense did not receive the information, which would have allowed them to suggest alternative killers to the jury.

She also said police had been told that Mulligan had a .25-caliber pistol he wore on his ankle, that a tipster claimed Mulligan’s girlfriend shot him, and that a woman was seen in his SUV before he was shot.

She said those were all pieces of information the defense could have used to suggest he was killed by someone who knew him.

Ball stressed in a footnote that the police department she criticized in her ruling is not the same as today’s department.

“In the twenty years after these events, this judge is acutely aware of the strides made by the Boston Police Department in the professional handling of the investigation and prosecution of their cases,’’ Ball wrote. “This is particularly true of the homicide department which is, deservedly, held in particularly high regard by this judge.’’

Because of reporting errors, a story in Thursday’s Boston Globe about a judge granting Sean K. Ellis a new trial in the 1993 murder of Boston Police Detective John Mulligan inaccurately characterized the role of ex-Boston Police Detective John Brazil. Brazil was immunized from prosecution in a corruption investigation by a federal judicial order in return for his testimony. Separately, a judge’s ruling did not implicate Brazil in an armed robbery that occurred 17 days before Mulligan’s death.


Evan Allen can be reached at evan.allen@globe.com. Follow her on Twitter @evanmallen. John R. Ellement can be reached atellement@globe.com. Follow him on Twitter @jrebosglobe.