A French judge's inquiry alleges the African country's current president masterminded the shooting down of a presidential plane in 1994. And he claims U.S. and U.N. officials worked to cover up the Tutsi leader's role.

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PARIS — More than a decade after the genocide, a mystery still lies at the heart of Rwanda’s soul.

But France’s most celebrated anti-terrorism magistrate believes he knows who assassinated two African presidents on April 6, 1994. The shooting down of the Rwandan presidential jet that night was followed by the slayings of an estimated 800,000 people, mostly members of the Tutsi minority.

In a report to French prosecutors late last year, magistrate Jean-Louis Bruguiere accused the Tutsi leader who is now president of Rwanda, Paul Kagame, of ordering the assassination.

The investigation includes allegations that U.S. and U.N. officials helped quash earlier inquiries to protect Kagame, an ally of the United States.

The French judge’s report, obtained by the Los Angeles Times, has caused an uproar in Africa and Europe, and led Kagame’s government to break off relations with France.

A U.N. tribunal is judging perpetrators of the genocide, but the ghosts of Rwanda still haunt a world community that failed to intervene. French investigators do not claim that the assassination was the sole cause of the genocide. Tensions had been growing between Tutsis and Rwanda’s majority Hutus. But Bruguiere alleges that Kagame sacrificed fellow Tutsis in a brutal “political calculation” aimed at toppling the Hutu-dominated government.

“Kagame deliberately chose a modus operandi that, in the particularly tense environment … between the Hutu and Tutsi communities, could only cause bloody retaliation against the Tutsi community,” says the judge’s report, which recommends that prosecutors file formal charges.

Former U.N. investigators who initially looked into the assassination told Bruguiere that their bosses had blocked efforts to pursue leads implicating Kagame. The 67-page French report presents testimony from exiled Kagame bodyguards, spies and commanders. They identified a commando team that allegedly shot down the plane, killing President Juvenal Habyarimana and the president of neighboring Burundi, as well as their aides and the French crew.

Warrants issued

In November, Bruguiere issued warrants for nine high-ranking Rwandan officials in the investigation, which he opened in response to a complaint from the widow of one of the French pilots. The judge also urged a U.N. war-crimes tribunal on Rwanda to investigate Kagame, who is immune from prosecution as a head of state.

The warrants put Rwandan suspects in danger of arrest if they travel, and Kagame also could be in jeopardy once he leaves office. But a trial in France seems remote for now.

In response to the warrants, Kagame accused the French of trying to conceal their ties to former Hutu leaders and said the prosecution amounted to blaming the victims.

“Mr. Bruguiere is an impostor, a politician,” Kagame said. “If he were a judge, he would raise the question of the implication of France in the genocide of the Tutsis in Rwanda.”

Bruguiere’s eight-year investigation led French detectives through a diaspora of Rwandan exiles in Africa, Europe and North America. It also revealed intrigue sometimes pitting France and its African allies against forces supported by the United States and Britain.

Bruguiere, 63, has ruffled diplomatic feathers before. He charged six Libyan intelligence officials, including the brother-in-law of the nation’s leader, Moammar Gadhafi, in the bombing of a flight from Zaire — now known as Congo — to Paris in 1989 that killed 170 people. A French court eventually convicted the Libyans in absentia.

Critics accuse Bruguiere of grandstanding and sloppiness. His report contains “disconcerting errors” such as misspelled names, Le Monde newspaper said. One of the witnesses, a former Kagame soldier living in Europe, has reversed his testimony and denied that he participated in shooting down the plane.

But a former chief U.N. investigator applauded Bruguiere for taking a new look at the case. The version of events advanced by the Rwandan government is that extremist Hutus killed the president as a pretext for launching the genocide, but Rwandan authorities have never charged anyone in the assassination.

“People feel very comfortable because there’s a version of history out there, they’ve published books, made films, and they feel comfortable leaving it alone,” said Michael Hourigan, an Australian who says he quit in disgust when ordered to stop investigating Kagame. “Someone needs to explain why there’s been no investigation.”

Former bodyguard’s account

Among the dozen Tutsi dissidents who testified in the French inquiry was Aloys Ruyenzi, a former Kagame bodyguard.

Ruyenzi, 35, says he fled to Europe because Rwandan operatives tried to kill him when he turned against the government.

He is one of many English-speaking Tutsis who grew up in Rwanda’s neighbor, Uganda. He received military training in Uganda and became an intelligence sergeant in a Rwandan exile force led by Kagame. He recalls with pride that he was chosen in 1992 as one of Kagame’s bodyguards.

Kagame led an incursion from Uganda, a U.S. ally, into Rwanda, where Hutu governments for years had repressed the Tutsis, often brutally. His crack 600-man guerrilla army forced a truce with Habyarimana, a Hutu with staunch French backing.

Ruyenzi said he stood guard on March 31, 1994, as Kagame and five top aides discussed shooting down Habyarimana’s plane. Col. Theoneste Lizinde, a military adviser, was a key plotter, Ruyenzi said.

“Lizinde was from Rwanda, not an exile, so he knew the territory more than the others,” Ruyenzi said. “Lizinde gave the report on where the plane should be shot. The place was near the airport. My testimony was not hearsay. I was an eyewitness. I heard what Kagame said. I was in the room. His quote was: ‘If the president does not die, we could not win the war.’ “

Ruyenzi and other witnesses testified that shoulder-borne Soviet-made SAM-16 missiles were smuggled to the area in a load of firewood. On April 6, a missile team infiltrated a Hutu-controlled semirural area near the airport in Kigali, the Rwandan capital, the report says.

Habyarimana and President Cyprien Ntayamira of Burundi returned together that evening from peace talks in nearby Tanzania. Their Falcon 50 jet descended into the sights of the commando unit about 8:25 p.m., according to the report. It names Sub-Lt. Franck Nziza as the fighter whose missile blew up the plane and sent flames and wreckage raining onto the presidential estate next to the airport.

“They came back … and said what they did,” Ruyenzi said. “They were promoted.”

Hours later, Hutu soldiers intercepted two radio communications, one in the presence of a U.N. peacekeeping officer, in which Kagame’s troops alluded to their success, investigators say.

French investigators later traced the missiles to a stock sold by Russia to Uganda, which provided them to Kagame’s troops, the report said.

Investigators say that rising hostility between Hutus and Tutsis before the assassination, as well as the downing of the plane, contributed to the genocide that followed. Extremist Hutus had been broadcasting venomous anti-Tutsi propaganda over the radio for weeks. But the investigators accuse Kagame of exposing Rwandan Tutsis to murderous retaliation by Hutus in a ploy to create chaos and seize power.

The prevailing theory

The Kagame government adheres to the contrasting theory that extremist Hutus angry about the peace deal with the Tutsis killed Habyarimana.

At first, that scenario shaped the thinking of Hourigan, the Australian former U.N. investigator, and his American deputy, retired FBI supervisor James Lyons, who were sent to the killing fields in 1996 to lead a multinational team.

“All the academic and press comment was that it was Hutus around the president,” Hourigan said. “But we never, ever met anyone who could give us substantive information to back up those leads.”

In early 1997, U.N. investigators developed three informants close to Kagame who implicated their leader.

“They had firsthand knowledge, and they said it had been a special unit that did black-bag jobs,” meaning covert killings, Lyons said in an interview. “Two of the informants knew each other, but the third didn’t [know either of them]. That lent credence to what they were saying.”

On March 7 of that year, Hourigan used a secure phone at the U.S. Embassy in Kigali, the Rwandan capital, to report to Louise Arbour, a war-crimes prosecutor based in The Hague, Netherlands, according to testimony.

Hourigan says the prosecutor encouraged him. But when he visited The Hague days later, he said, she ordered him to drop the investigation of Kagame.

Arbour, now the U.N. high commissioner for human rights, has declined to comment.

Hourigan said in his testimony that he suspected U.S. spies learned about the emerging focus on Kagame and that Washington, D.C., leaned on U.N. brass to protect the Tutsi leader.

U.S. officials who served under President Clinton say it is farfetched to think Washington helped quash the investigation. But Herman Cohen, the assistant secretary of State for Africa under President George H.W. Bush, said the idea is plausible because U.S. officials felt guilty about failing to intervene in the genocide.

“The Clinton administration really did everything possible to protect Kagame,” Cohen said.

Cause and effect

Everard O’Donnell, a spokesman for the U.N. genocide tribunal, based in Arusha, Tanzania, declined to comment on that debate. But he said Hourigan’s internal report has remained available to prosecutors.

O’Donnell said the trials so far had contradicted the idea that the assassination triggered the genocide.

“The whole point about the genocide is that it was planned, pre-planned,” O’Donnell said. “Although the crash, the killing of the presidents, plays a role, it is not the cause of the genocide.”

As for the accusations against Kagame, O’Donnell said the evidence is mixed. “The position is very much today that it’s a whodunit,” he said. “And we don’t know whodunit.”

In a chilling footnote, two potential witnesses identified by the U.N. investigative team were killed in Nairobi, the Kenyan capital, team officials and French investigators say.

Lizinde, named as a lead plotter, was kidnapped and slain in 1996 as he prepared to write a book about the assassination, the French report says. His family accuses Rwandan agents of the killing, citing documents in which Lizinde said he fled to Zaire and then Kenya after being targeted by Kagame’s forces, the report says.

The other man slain was former Interior Minister Seth Sendashonga. Kenyan police accused a Rwandan diplomat of trying to kill him in 1996 and deported the official; Sendashonga was slain two years later.

A former Rwandan military intelligence agent living in exile in the United States testified that the killing was the work of a covert unit created to silence dissidents.