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A woman holds up flowers and an image of late prosecutor Alberto Nisman while waiting for the hearse with his remains, in Buenos Aires January 29, 2015. Argentine prosecutor Nisman who died under mysterious circumstances the day before he was to testify in Congress about allegations against the president regarding an investigation into a 1994 bombing, was buried on Thursday amid calls for justice.MARCOS BRINDICCI/Reuters

Was the death of Alberto Nisman intended as a message? And if so, who sent it? After two weeks of near-unceasing drama, this uneasy question hovers over the Argentine capital.

Mr. Nisman was a special prosecutor tasked with investigating one of the most brutal terror attacks in Latin American history. He was found dead on Sunday of a gunshot wound in the bathroom of his elegant Buenos Aires apartment. He had been set to testify on Monday to Congress about charges he filed implicating President Cristina Fernandez de Kirchner, her Foreign Minister and political aides in a plot to cover up Iranian responsibility for the suicide truck bombing of a 1994 Jewish community centre here that killed 85 people.

Police are investigating whether Mr. Nisman killed himself or was murdered, a question still not answered to anyone's satisfaction. Ms. Fernandez de Kirchner first vigorously proclaimed his death a suicide – and now just as fiercely says he was murdered. Few Argentines are likely to trust any official conclusions in the case, given this country's history of political state violence and how deeply the government's tentacles still reach into the police and the judiciary.

But in cafés beneath bright awnings, and at scarred wooden tables in parilla steakhouses, theories are debated intensely. The cast of potential suspects includes assassins sent by the President or her allies to eliminate a critic and frighten others following his work; the Lebanese militant organization Hezbollah seeking to shut down the investigation of its patron, Iran; and the President's own latest favourite that Mr. Nisman died at the hands of rogue agents from Argentina's shadowy domestic spy service.

The theories are so complicated, and sometimes so lacking in logic, that it is difficult to imagine them being floated, let alone seriously debated in endless television coverage, in any country but this one,so steeped in political division and dark history.

If it was murder, carried out on the watch of an elite security detail, the specific message remains opaque. But the larger tactic is perfectly clear, and it has unsettled many Argentines, stirring dark memories of an era they had hoped they were leaving behind.

"It's like a signal: nobody else investigate power," said Patricia Bullrich, spreading worried hands across her dining room table. "It's like when drug traffickers send a message: stop here or you will be next."

Ms. Bullrich, an opposition member of Congress from a patrician family with shifting political ties, chairs the parliamentary committee that had called Mr. Nisman to testify. She spoke to him two days before he died, and recalled in an interview this week that he seemed utterly normal – just tired, a bit worried. Not remotely suicidal.

She is among those who believe his accusations against the President had merit. She says she knows he built the case on 5,000 hours worth of wiretapped telephone conversations. "But I can't imagine the President gave the order to go and kill him," Ms. Bullrich added, her brow creased with anxiety beneath heavy auburn bangs.

Plenty of other powerful people, however, might have been keen to silence Mr. Nisman to demonstrate the price of asking questions. It's a blunt-force mode of communication in a country where most people have vivid memories of life under dictatorship. "It's the return of political violence," Ms. Bullrich said. "That is the feeling. Can you sense it?"

The prosecutor's death is profoundly damaging for Argentina, where an air of progress on some key national issues has been sharply undermined by the tumultuous events of the past few weeks.

Mr. Nisman, known as a hard-working federal prosecutor with a tendency for the occasional grandstanding accusation, took charge of investigating the AMIA bombing – it is known by the name of the community centre – in 2004. It was already a politically charged file. In the late 1990s, a group of Argentinian police officers and others were brought to trial on charges of assisting in the bombing, but were acquitted after the judge and investigators were found to have faked evidence and bribed witnesses. A new series of indictments alleges those irregularities extended all the way to the office of former president Carlos Menem, who is among eight people expected to go on trial for obstruction of justice in that case in June.

Then, on Jan. 14, Mr. Nisman filed a stunning charge sheet with a judge. President Fernandez de Kirchner and Foreign Minister Hector Timerman, he said, had conspired with Iranian officials to cover up the role of Iranian nationals in the bombing. The allegation is that they subverted the course of a nationally important investigation – in effect, as a senior legal official described it in an off-the-record conversation about the charges, they committed treason.

Mr. Nisman said that he had uncovered hints of the alleged plot in the course of his AMIA work, and it so disturbed him he had no option but to pursue it. Essentially he said that Ms. Fernandez de Kirchner, eager to build ties with Iran and bolster an economy crippled by her government's policies, made a secret deal with Iran to cover up Iranian involvement in the bombing. That deal, he charged, was made before the countries publicly agreed in 2013 to work together on a so-called Truth Commission to investigate the attack.

Under the secret deal, Mr. Nisman alleged, said Argentina would drop the Interpol notices for seven Iranian suspects in the bombing, and redirect its investigation away from Iran, likely onto a local fascist organization. In exchange Argentina would trade food for Iranian oil. The pact was allegedly brokered by aides including Luis D'Elia, a provocative left-wing social activist who dealt with Mohsen Rabbani, the former Iranian cultural attaché in Buenos Aires who some believe was the mastermind of the bombing.

Ms. Bullrich compares it to the idea of a U.S. president conspiring with Osama Bin laden on a 9/11 truth commission; she called it "a very dark, illegal negotiation with people not in government."

Reactions to the Nisman charge cleaved along political lines, in accordance with the roughly equal parts admiration and loathing inspired by President Fernandez de Kirchner, a champagne socialist with a flair for populism and a fierce with-me-or-against-me political ethic.

Those who hate the President, and there are many, are fully prepared to believe she ordered the prosecutor killed. "She has a sick hunger for power and to keep it she is capable of anything," said Gabriel Levinas, author of a book about the bombing and commentator on a prominent current-affairs program with the Clarin media group, with which she has battled.

Supporters of the President reject the Nisman indictment as legally flimsy and full of fantastic and baseless allegations. A former Interpol chief has said that the Argentine government never tried to get the warrants on the Iranians lifted, noted Horacio Verbitsky, a prominent investigative journalist who also heads a human rights organization. He also pointed out that Argentina does not import the petroleum products Iran sells. In an interview in his book-lined living room, he waved a copy of the Nisman denuncio, fringed in Post-it notes, then threw up his hands. "It's self-contradictory and rebuffed by reality. It's an impossible crime."

Ms. Fernandez de Kirchner, first in a rambling, conspiratorial post on her website and then later in a televised address in which she wore stark white and sat in front of the pale blue Argentinian flag, has advanced the theory that rogue spies were using Mr. Nisman. "Someone planted fake information in Nisman's report," wrote much of the charge sheet and eliminated him once he had done the service of smearing her and creating a political crisis, she said.

Certainly there is bad blood between her and certain spies. Late last year, Ms. Fernandez de Kirchner fired the operations director of the intelligence secretariat, Antonio Stiuso – possibly, some now speculate, because she learned he was working with Mr. Nisman. He was once a presidential ally who, human rights groups say, supervised an effort to spy on her political opponents. But his relationship with Ms. Fernandez de Kirchner had cooled, in part because of her friendly relationship with Iran. The Argentine intelligence services have worked closely with the CIA and the Mossad in the past. (Argentina has the largest Jewish population on the continent, some 220,000 people, and many have ties to Israel.)

The speculation over Mr. Nisman's death has produced convoluted theories from all quarters. Ms. Fernandez de Kirchner has suggested that Mr. Stiuso, angered at his firing, took his revenge by pressuring Mr. Nisman to make manufactured charges against her public this month and then arranged his death, or threatened him into suicide, before he could expose the plot. Mr. Stiuso has not made any public comment.

Analia Del Franco, a political analyst who is not a champion of the President, says that theory is plausible. "I think the intelligence services killed him to give the government a body to deal with. His death is worse for government than if he had gone on filing complaints," she said. "But one of the most important unanswered questions is – why did he let himself be manipulated?"

There are also many people here who believe that foreign operatives, for example an organization such as Hezbollah, might have carried out the killing. Or, some say, the murder might be timed to amplify negative attention on Iran, by agents of a foreign government; dark hints about Mossad come up often here.

The only shred of good news in the whole mess, said Mr. Verbitsky, whose organization has sued government on behalf of the bombing victims' families, is that the President has pledged to dissolve the existing intelligence service. It operates almost unchanged from what it was during the dictatorship, when it oversaw the disappearances of 30,000 people. Ms. Fernandez de Kirchner says it will be replaced by a new federal agency under tighter civilian control.

Ms. Bullrich, the opposition politician, said she expects the shift will be cosmetic. "This is the intelligence agency that was with this government for 12 years," being used by Ms. Fernandez de Kirchner, and her late husband, former president Nestor Kirchner before her, against the media and political opponents, she said. "For 12 years she had the chance to make reforms and never did it."

Mr. Verbitsky hopes for real change. In recent years, Argentina has achieved important things, he said – prosecuting senior police and military officials for dictatorship-era human rights abuses, bringing the military fully under political control, resolving its foreign debt crisis. But now that momentum has been checked. "This doesn't do any good to Argentina has a whole, and it's a pity."

With new developments each day, it is impossible to calculate a long-term impact. Ms. Del Franco said that national elections in October are too close to predict – Ms. Fernandez de Kirchner cannot run again – but that the next eight months give her party time to ride out the scandal. But she, too, spoke of a larger damage, to the country's reputation and even its national psyche.

"This is still a very vulnerable society, and there is power much higher than the official one," she said. "The principal importance of this event is that it's a sharp reminder of the power in the shadows."

The Investigation

New claims and counter-claims about Alberto Nisman's death are made each day, but the basic outline appears to be this: that Mr. Nisman's 10-person security detail saw nothing, and didn't try to check on him for nearly eight hours although he did not answer their phone calls from outside his apartment.

The gun that killed him was a .22-calibre Bersa lent to him on the day before he died by an IT technician named Diego Lagomarsino. The apartment was locked from the inside, although it may have been possible for someone to get in a back door.

Prosecutor Viviana Fein has confirmed that the gun that killed Mr. Nisman was fired within one centimetre of his skull, and that the autopsy showed no evidence of struggle. She has charged Mr. Lagomarsino with supplying Mr. Nisman with a weapon for which he did not have a licence.

In a wild-eyed news conference on Wednesday, Mr. Lagomarsino countered that his boss was terrified for his life, that his daughters were also afraid of spending time with him because of threats, and that he had been warned he could not trust his own bodyguards.

Mr. Nisman's family and friends say he was anxious about the investigation, but far from suicidal – he left no note, and spoke hours before his death with colleagues about plans for the Congressional appearance. His ex-wife has formally registered a case rejecting the suicide thesis.

If it was suicide, friends have told reporters, it must have been "induced," perhaps because someone was threatening the life of his teenage daughters – his life, or theirs.

"The evidence looks like suicide but other elements make that hard to believe: they suggest murder and it's very difficult to untangle," said a senior official with close knowledge of the investigation into Mr. Nisman's death. He was not authorized to speak on the record. "Even if you can show in court it's suicide, 90 per cent of people will think it's murder anyway, because they are accustomed to doubting the official line on things like that."