Now that the dust is settling, we're looking at the fallout from the revelation Monday that there will be no new trial for Sean Ellis, the Boston man who was serving life in prison but was freed three years ago. A judge ruled in 2015 that corruption among the investigating officers raised questions about the fairness of Ellis' conviction. WGBH Radio's Phillip Martin has been following the story closely. He spoke with WGBH All Things Considered host Barbara Howard. The following transcript had been edited for clarity.

Barbara Howard: It all started back in 1993 with the murder of Boston Police Detective John Mulligan. So talk about what happened then.

Phillip Martin: John Muilligan was a detective who worked a lot of details, and some of those details included working outside of a Walgreen’s in Roslindale, right off of the American Legion Highway. One morning at 3:30 a.m., he was found by a Walgreen’s employee, slumped in the car. He had apparently been shot five times. Police later determined or said that those involved were two individuals, a fellow named Sean Ellis and a friend of his, Terry Patterson, who had gone to the drugstore that morning.

Howard: Ellis ended up going on trial, and he served about half his life in prison, 22 years. He’s now 45 years old. He insists that he did not kill Detective Mulligan. But how did it come about that he was tried three different times?

Martin: The jury in the first two trials simply did not believe the police version of events. Also, a key witness, a woman named Rosa Sanchez, misidentified Ellis and Patterson and finally settled on them as the suspects after she had met with the investigators who happened to know the key witness in this case. So the key witness knew the investigators working on this case, and for many, that seemed problematic.

Howard: What was the victim’s reputation, Detective Mulligan?

Martin: Mulligan was both known as someone who worked details and was helpful on the streets, but was also known as someone who was corrupt.

Howard: In what way?

Martin: As someone who was involved in robbing drug dealers and assisting the other police officers who later were tried in a separate trial of corruption. He was tied to this ring of corruption, if you will.

Howard: Yesterday, at the press briefing, the Boston police commissioner, William Gross, along with the Suffolk County district attorney, John Pappas, acknowledged that there was corruption — that three detectives, Acerra, Robinson and Brazil, were corrupt. They were the investigating detectives of the death of Mulligan. But DA Pappas was still maintaining that the corruption had no bearing on the case against Ellis.

Here’s what Pappas said just yesterday:

"There’s no reliable evidence that Acerra, Robinson or Brazil procured or produced false evidence in this case," Pappas said. "We don’t believe Detective Mulligan was involved in their schemes."

Howard: So prosecutors dispute the idea that Mulligan was involved with the corruption linked to those officers. Can you talk about that?

Martin: Well, this is demonstrably untrue, as determined by researcher Elaine Murphy with the Schuster Institute for Investigative Reporting. They found FBI documents and multiple eyewitnesses. In the Ellis retrial of 2013, grand jury testimony of a drug dealer, Robert Martin, placed Mulligan at the robbery of his Commonwealth Avenue apartment with Acerra and Robinson 17 days before the murder. This was the telling piece of evidence that finally linked Mulligan to corrupt cops.

Howard: So you’re saying that Mulligan, prior to his death, was involved with Acerra, Robinson and Brazil, who were the three detectives who would investigate Mulligan’s own death.

Martin: That’s right. Sean Ellis’s attorney, Rosemary Scapicchio, who has been working on this case for a long time and is credited with getting him to where he is today, that is to say, out of prison, talked about the fact that the Boston Police and the DA’s office should have known about this corruption.

"I think that the evidence led in a bunch of different directions and they knew it, and that there were other people that are culpable out there," Scapicchio said. "I’m hopeful that they continue their investigation and they find the person who really did kill Detective Mulligan."

Howard: Now for Ellis, it’s pretty much behind him. Have you had a chance to talk with him since he’s learned that he’s not going to be tried again, that he’s essentially a free man?

Martin: I have. I spoke with him at his lawyer’s office.

Here’s what Ellis said:

"I’m not the only one that has gone through this horror," Ellis said. "Wrongful convictions is an epidemic."

Howard: Is he at all bitter?

Martin: Not at all. He’s living at home with his mother and sister under the same roof in Lynn, trying to get on with his life — working a job full-time and planning to go to the university now that this case is behind him.

Howard: And what about the victim’s family, the family of Detective John Mulligan?

Martin: As you can imagine, there’s still a lot of anger. Richard Mulligan, John Mulligan’s brother, remains convinced that Ellis murdered his brother, but is not keen to talk to most reporters about this case.

Howard: That’s WGBH Radio’s Phillip Martin, telling us about the case of Sean Ellis. Ellis was convicted of the 1993 murder of Boston Police Detective John Mulligan. Ellis was freed three years ago amid questions about officer corruption. Now, prosecutors say that they will not seek a new trial. This is WGBH’s All Things Considered.