He died as he lived, in a miasma of mystery carrying a whiff of violence, death and deceit.

The only public certainty seemed to be a stubborn denial by Freddie Scappaticci that he had ever been a double agent with the code name Stakeknife — the British Army’s highest-ranking mole in the insurgent Irish Republican Army during the Northern Ireland sectarian conflict known as the Troubles.

Word of his demise began to emerge in recent days as many people, including President Biden, gathered in Ireland to celebrate the 25th anniversary on April 10 of the Good Friday Agreement that set Northern Ireland on course for a still imperfect peace.

“We were made aware last week of the passing of Frederick Scappaticci,” Jon Boutcher, a former chief constable in the British police who is leading a protracted inquiry into the Stakeknife imbroglio, announced on April 11.

The usual details of an obituary — the date, location and cause of death — were missing. Even Mr. Scappaticci’s age was uncertain.

By the time his death became known, British news reports said, he had already been buried at an undisclosed location. He was in his mid-to-late 70s and had been living under a witness protection program, these reports said.

Perhaps fittingly, Mr. Scappaticci’s death conjured one of the darkest, deepest unsolved mysteries of a war, fought publicly and in the shadows, that took more than 3,000 lives in three decades of sectarian bloodletting. The conflict drew in Catholic Republicans seeking a united Ireland, Protestant loyalists fighting for continued ties to Britain, and the British authorities that control Northern Ireland.

Mr. Scappaticci, a former bricklayer, led the Irish Republican Army’s internal security unit for more than a decade. He was accused of overseeing the torture and killing of more than 30 suspected informers. If, at the same time, he was the British mole called Stakeknife, then he was a paid British agent killing fellow British agents.

Mr. Scappaticci may well have taken some of his secrets to his grave, shielding government intelligence and military handlers from one of the central moral conundrums of the case: Did the British state collude in the killings in order to protect Stakeknife’s identity?

British officials have described Stakeknife as the “golden egg” and “the jewel in the crown” of their infiltration of the I.R.A. They have said that intelligence he delivered alerted them to myriad I.R.A. operations, saving hundreds of lives.

For the I.R.A., the case has the potential to revive a deep humiliation at being so duped by its British adversaries.

Mr. Boutcher’s protracted and oft-delayed inquiry, begun in 2016, aims to resolve these questions. His statement said “that people may now feel more able to talk” about Mr. Scappaticci now that he’s gone, and asked “anyone with information” to come forward.

The case has assumed particularly lurid overtones because of the extreme violence it involved. Stakeknife had penetrated the heart of the I.R.A.’s internal security unit, known as the Nutting Squad, a macabre sobriquet evoking the unit’s standard operating procedure — the execution of accused informers with two bullets to the “nut,” or head. Bodies were usually then dumped.

It is unclear how many other informers were reporting the I.R.A.’s inner workings to the British.

“You can’t rule out the real possibility that within that unit there were other persons who had informant status,” Kevin Winters, a lawyer representing 12 families of the I.R.A.’s victims, told The Sunday Times of London, referring to the so-called Nutting Squad.

But Mr. Scappaticci’s death may also mean that time is working against an unraveling of such mysteries.

“The very nature of historical investigations will mean a higher likelihood that old age may catch up with those affected,” Mr. Boutcher said in the statement, “be they perpetrators, witnesses, victims, family members or those who simply lived through those times, before matters are concluded.”

Alfredo Scappaticci was born in a staunchly Republican area of Belfast in the mid-1940s, the descendant of an Italian family that had immigrated to Northern Ireland in the 1920s and founded a business selling ice-cream. He was known variously as Scap and Freddie.

As a zealous soccer player, he was said to have tried out for a British club, Nottingham Forest, but returned to Northern Ireland to become a bricklayer. He married Sheila Cunningham, with whom he had six children. Ms. Scappaticci died in Belfast in 2019, according to Irish news reports.

No information about survivors was available.

In 1969, Britain deployed armed forces in Northern Ireland to try to tamp down sectarian violence. One tactic was internment without trial, mainly of suspected Republican activists, at a former Royal Air Force based outside Belfast, then known as Long Kesh.

In 1971, Mr. Scappaticci was among those detained along with such dominant figures of the Republican movement as Gerry Adams, who later became head of Sinn Fein, the political wing of the I.R.A. When Mr. Scappaticci was freed after three years of detention, he had, by most accounts, become a committed foot soldier of the I.R.A., destined for rapid promotion in its internal security unit.

According to Martin Ingram, the pseudonymous co-author of “Stakeknife: Britain’s Secret Agents in Ireland,” published in 2012, Mr. Scappaticci “volunteered his services to British Army intelligence in 1978.” Several accounts say he made his move to seek revenge after fellow I.R.A. operatives gave him a severe beating for poor discipline.

Mr. Ingram wrote that until 1996 — two years after the I.R.A. declared a cease-fire — “Scappaticci would have a role in investigations into suspected informers; inquiries into operations suspected of being compromised; debriefings of I.R.A. volunteers released from questioning; and vetting of potential recruits.”

At the same time, though, Mr. Ingram said, Mr. Scappaticci was on the British payroll as an agent. Stakeknife was said to have been paid 80,000 pounds a year, the equivalent of more than $300,000 in today’s money.

“Stakeknife produced high-grade intelligence, much of it read at the highest levels of the political and security establishments. He was without doubt the jewel in the crown,” Mr. Ingram wrote. “The problem was, Stakeknife could only shine if he immersed himself in the activities of those he was reporting upon, including murder and other illegal acts.”

In 2003, several British newspapers identified Stakeknife as Mr. Scappaticci. He denied the accusations publicly but then dropped out of sight. Several news reports said the British authorities had spirited him away, first to the Italian town of Cassino and then to a witness protection program in Britain.

In his 2012 book, Mr. Ingram provided a more a definitive identification of Mr. Scappaticci as Stakeknife and named 35 victims of the Nutting Squad in the period when Mr. Scappaticci was associated with it. Mr. Ingram said his nom de plume was meant to shield his identity as a former member of the Force Research Unit, the undercover British organization that ran Stakeknife as a mole.

Mr. Boutcher, the head of the Stakeknife inquiry, promised on April 11 that investigators would publish an interim report on their findings this year. But families of victims greeted the news with skepticism.

“Clearly the death will have an impact on both the content of the report and whether or not criminal prosecutions go ahead,” Mr. Winters, the relatives’ lawyer, said. “Families of victims will rightly ask questions.”