How CIA Trained and Used Paul Kagame to Unleash the 1994 Rwandan Genocide

Just after 8 p.m. on the night of April 6, 1994, two surface-to-air missiles, fired from a location near Kigali airport, struck the Dassault Falcon 50 private jet of Rwanda’s Hutu President Juvénal Habyarimana.

Kagame leading his men in battle. [Source: newsweek.com]

By Jeremy Kuzmarov

  • Jeremy Kuzmarov is Managing Editor of CovertAction Magazine. He is the author of four books on U.S. foreign policy, including Obama’s Unending Wars (Clarity Press, 2019) and The Russians Are Coming, Again, with John Marciano (Monthly Review Press, 2018). 

After an explosion, the plane crashed just yards from Habyarimana’s home, with his kids watching in horror from their garden.

Habyarimana had been returning from a conference in Arusha, Tanzania, where a power-sharing agreement had been signed a year earlier between the Hutu and Tutsi.

Habyarimana died in the crash along with Burundian President Cyprien Ntaryamira, Major General Déogratias Nsabimana, Chief of Staff of the Rwandan Army, six other government officials and a three-man French crew.

Within hours of the assassination, the Rwandan genocide commenced as Hutu militias (Interhamwe) began slaughtering Tutsis and Hutu moderates, while the Tutsi-led Rwandan Patriotic Front (RPF), led by Major General Paul Kagame, advanced its drive to seize power.

The Clinton administration and mainstream media at the time blamed Hutu extremists led by Colonel Théoneste Bagosora for shooting down Habyarimana’s plane, which BBC journalist Mark Doyle called “one of the great mysteries of the 20th century.”

Remains of plane carrying Rwanda’s President Juvénal Habyarimana whose death triggered the 1994 genocide in Rwanda. [Source: bbc.com]

Rwanda had been in civil war since October 1990, when the RPF invaded Rwanda from Uganda in an attempt to unseat the Hutu-dominated government, which had expelled the Tutsi who had allied with the Belgian colonialists prior to Rwanda’s independence in 1962.

A problem with the official story was that the Tutsi represented a minority in Rwanda, and the power-sharing agreement concluded at Arusha would have left the Hutu with majority power.

The Roman philosopher Seneca once stated that “the one who derives advantage from a crime is the one most likely to have committed it.”

The main beneficiary in this case was the Tutsi-led RPF and Major Kagame, who seized power after Habyarimana’s death and has held onto it ever since.

When asked about Habyarimana’s death in 2006, Kagame responded: “I don’t care,” noting that Habyarimana had made him grow up as a refugee, and that he was justified in fighting his government.

Jim Lyons, an FBI Special agent who was assigned the task of investigating the crash as part of a UN team, stated “what better way for Kagame to become a hero than to start the genocide himself by shooting down the plane and then marching into Kigali with his army and saving everybody.”

All Evidence Points to Kagame

An eight-year investigation by French magistrate Jean-Louise Bruguière, along with other independent investigations including one by a UN-appointed team, concluded that Kagame and the RPF shot down Habyarimana’s plane, and launched a planned and coordinated assault on the Rwandan government afterwards.

The Rwandan army was found to have had radio signal intercepts recording an RPF commander stating that “target is hit” after the crash. In October 2011, Kagame’s former aide Theogene Rudasingwa stated that Kagame told him “with characteristic callousness and much glee” that he ordered Habyarimana’s plane shot down.

Kagame’s former military chief of staff, Faustin Nyamwasa, who was one of nine indicted following Bruguière’s investigation, and six other high-ranking RPF officers, have also testified that Kagame ordered the shootdown of Habyarimana’s plane.

Among them is former RPF Captain Frank Tega, who claims that he was with Kagame and others at Kanombe in late July 1994 when they were having drinks and boasting about the RPF’s killing of Habyarimana.

Kagame’s former bodyguard James Munyandinda, who had been charged with guarding the missiles, said that two RPF commandos, Eric Hakizimana and Frank Nziza, admitted to him in July 1994 that they had brought the missiles to Masaka and fired them at Habyarimana’s jet.

Juvénal Habyarimana [Source: rte.ie]

FBI Special agent Jim Lyons said that RPF informants told him during his investigation that a network of agents put together by Kagame had plotted to shoot down the presidential aircraft, and that there was no evidence that the Hutu government was behind it.

The Rwandan government, led by Kagame, has claimed—based in part on an investigation carried out by researchers at the UK Defense Academy—that the missiles had to have been fired near the Kanombe military camp, the President’s home, and the main Kigali airport, and this entire area was completely controlled by the Rwandan army.

However, the RPF could easily have infiltrated the area, as the Bruguière investigation concluded, and had experience shooting down aircraft (it shot down at least four during Rwanda’s civil war).

The missiles recovered shortly after the crash were Russian-made SA-16 missiles, which the RPF—and not the Rwandan army—was known to possess.

Later the weapons—which Nyamwasa said were originally smuggled into Rwanda under a load of firewood—disappeared but were eventually seized by rebel forces in Congo and turned over to the UN.

Belgian historian Filip Reyntjens found that the serial number was identical to a missile that had been fired by the RPF in May 1991 but had failed to explode.

About three weeks after the crash, local farmers found two SA-16 missile launchers in a valley near Masaka Hill within range of the airport that was accessible to the RPF.

According to the Russian military prosecutor’s office, the launchers had been sold to Uganda by the USSR in 1987.

French army Captain Paul Barril, who served as an adviser to Habyarimana, claimed that the SA-16s had Iraqi numerical markings and that after Operation Desert Storm, the CIA transferred the missiles to the RPF from seized Iraqi arms caches.

The warehouse where they were stored, and then re-assembled in Kigali, was rented by a Swiss front company tied to the CIA, according to a whistleblower’s report published on the website intabaza.com.

French Foreign Minister Alain Juppé and Defense Minister François Leotard also claimed that members of the RPF received specialized missile training near Phoenix Arizona, which would indicate direct American complicity.

Jean-Louise Bruguière told Boutros Boutros-Ghali, the UN Secretary-General at the time, that the CIA “was involved in the shootdown,” adding strength to Boutros-Ghali’s earlier statement that the Americans were “100% responsible for the Rwandan genocide.”

Christopher Black, the lawyer for Augustin Ndindiliyimana, chief of staff of the Gendarmerie under Habyarimana who was acquitted of war-crimes charges, alleged that Canadian General Romeo Dallaire, Commander of the United Nations Assistance Mission for Rwanda (UNAMIR), arranged for one axis of the runway at the airport to be closed at the request of the RPF, making it easier to shoot down the plane as it tried to land.

Significantly, after the plane crash, Kagame’s RPF forces circled around Kigali rather than heading south where most of the Interhamwe killings were taking place.

Child looks upon dead in Kigali killing during Rwandan genocide, July 1994. [Source: ncronline.org]

The RPF carried out major massacres, with Kagame and his henchmen setting up open-air crematoria to dispose of the bodies efficiently.

According to Luc Marchal of UNAMIR, the RPF’s military maneuvers had to have been pre-planned over weeks or months, and could not simply have been in reaction to the first massacre of Tutsi, as the RPF claimed.

Many Other Deaths

In 2007, an RPF defector writing in the Uganda Free Press, claimed that members of the RPF team that shot down President Habyarimana’s plane were all killed in order to erase evidence of the crime.

Two members of the crew—Private Joseph Nyamtale and Bosco Rumenera—were hacked to death at a roadblock immediately after fleeing from the scene.

The defector said that he survived based on luck after escaping from detention because of a careless guard, and fled to Uganda.

Journalist Judi Rever reported on the killing of Christophe Kayitare, who was allegedly stationed at the airport control tower to signal the arrival of Habyarimana’s plane and communicated with the missile team in Masaka, and Eric Leandre Ndayire, whose sister’s home was used to hide the missiles used in the attack.

On April 7, 1994, Hutu Prime Minister Agathe Uwilingiyimana was killed in her home in an assassination that has never been properly investigated.

On July 1, 1996, Tanzania’s former director of security intelligence, Major General Imran Kombe was shot dead by policemen in Noshi in northern Tanzania after he had exited his car and showed police he was unarmed.

Prior to the April 6th shootdown of Habyarimana’s plane, Kombe had been tipped off about a possible assassination attempt against three leaders who were to have attended the Arusha conference—Habyarimana, Kenyan leader Daniel Arap Moi, and Congolese leader Joseph Mobutu.

It is thought that Kombe tipped off Moi, who then relayed the warning to Mobutu. Intelligence sources suggested that Kagame was the mastermind behind Kombe’s killing.

In 2010, former Rwandan army chief Faustin Nyamwasa, who implicated Kagame in the killing of Habyarimana, survived an assassination attempt when shots were fired at his car in the driveway of his Johannesburg home. As he recovered in the hospital, another group of assailants tried to sneak into his room and strangle him with string.

In 2014 his house was broken into, leading South Africa to expel Rwandan diplomats from the country after linking its intelligence agents to the raid. Nyamwasa told The Associated Press that Kagame has hunted him and other dissidents around the world, “using hired killer squads.”

One of the victims of these squads was Colonel Theoneste Lizinde, an RPF defector who said he attended a planning meeting for the presidential plane shootdown and implicated Kagame as the mastermind of the criminal plot.

Lizinde was assassinated in 1998 in Nairobi by agents from Rwanda’s foreign intelligence service, which was commanded at the time by Patrick Karegeya, who was himself strangled to death by Kagame’s hit squad at a hotel in Johannesburg on December 31, 2013.

After Karegeya’s death, Kagame’s Minister of Defense said that “when you chose to be a dog, you die like a dog, and the cleaners will wipe away the trash so that it does not stink for them.”

In the 2014 BBC documentary “Rwanda’s Untold Story,” Nyamwasa referred to Kagame—whom Bill Clinton once praised as “one of the greatest leaders of our time”—as a “serial killer,” while a former development worker characterized Kagame as the “devil,” and his regime as “pure evil.”

Patrick Karegeya, the RPF’s former intelligence chief. He too had identified Kagame as Habyarimana’s assassin. [Source: southerneye.co.zw]

The victims of Kagame’s hit squad have included his personal doctor, Gustave Makanon, and driver, and a popular gospel singer, Kizito Mihigo.

A senior regime official said that he once saw Kagame personally beat a colleague with sticks for buying curtains from a store not owned by the ruling party, which has vast assets and is controlled by Kagame. The victim was then sent to prison where he remained for nearly a decade.

In November 2014, Emile Gafirita (a.k.a. Emmanuel Migisha), was kidnapped in Nairobi and “disappeared” just before he was scheduled to travel to France to appear before Judges Marc Trévidic and Nathalie Poux to testify about the Habyarimana killing.

Gafirita had served as a child soldier in the RPF and purported to have insider knowledge about the plane shootdown. He is yet one more victim of the events of April 6, 1994, whose toll in human lives is staggering.

Fair-Haired Boy of the U.S. Government

Despite his long record of brutality, Kagame was for years lionized in the Western media, granted honorary degrees at prestigious universities including Harvard, feted by Hollywood celebrities, and in 2009 made the  “Time 100” list of the world’s most influential people.

This was all part of a publicity campaign orchestrated by U.S. intelligence agencies.

Jim Lyons, the former FBI agent, has testified that Kagame was the “fair-haired boy of the U.S. government and the Brits, trained by the CIA and MI6.”

After the RPF invaded Rwanda illegally in October 1990, American aid was funneled through the RPF’s sponsor in Uganda, which purchased ten times more weapons in 1991 than in the preceding 40 years combined.

Roger Winter, head of the U.S. Committee for Refugees (USCR) and a suspected CIA agent, was decorated by Kagame at the July 4, 2012, celebration of the 16th anniversary of the RPF’s victory in Rwanda.

In the early 1980s, Winter had supported the National Resistance Movement (NRM) in Uganda led by Yoweri Museveni, Uganda’s current leader, Kagame and the Hemi Tutsi elite, who fought against Uganda’s then-President Milton Obote, a one-time socialist.

For the remainder of the decade, Winter worked to advance the militant plans of the Rwandan Tutsi elite, which had been expelled from Rwanda when the Hutu took over in the 1960s.

Winter helped establish USCR funding for RPF propaganda tracts and the RPF’s journal, Impuruza running from 1982 to 1994, which dehumanized the Hutu people, and organized a major conference of Tutsi exiles in Washington, D.C., in 1988 where a military solution to the Tutsi problem was decided.

In 1992, Winter put Kagame in touch with high-ranking bureaucrats in the U.S. State Department and allegedly briefed Clinton administration officials of the RPF’s military achievements when he was on the war’s front lines.

According to Bernard Lugan, a French historian and editor of the online journal L’Afrique Réelle, Winter was present at Kagame’s headquarters at Mulundi [in Rwanda] on the night of April 6,1994, when the plane crash occurred.

Kagame had learned many tricks of his trade fighting in the Ugandan bush war of the 1980s, where he earned a reputation for inflicting torture as an National Resistance Army (NRA) military intelligence officer.

Roger Winter at this time was promoting low-intensity warfare methods, including psy-ops in which NRA guerrillas disguised as government forces committed atrocities, and Obote was accused of committing genocide.

Kagame never forgot how the tide in the war had turned when one of Obote’s top commanders, David Oyite-Ojok, had his helicopter shot down.

Kagame took control of the RPF following the October 2, 1990, assassination of RPF commander Fred Rwigyema, which Kagame is suspected of being behind.

Hundreds of RPF guerrillas were subsequently executed in internal ethnic fighting, with the victims’ bodies dumped into the Akagera River.

Abdul Ruzibiza, an RPF veteran, stated that “Kagame found himself at the head of an army that did not accept him. He maintained his rule through terror, assassination, imprisonment and executions.”

When Rwigyema was selected by Museveni to attend an officers’ course at Fort Leavenworth, Kansas, Kagame went in his place and was trained in the art of psychological warfare and other counterinsurgency tactics including the art of deception.

Kagame has since honed these tactics to perfection, staging atrocities repeatedly and blaming the Hutu for them while slandering anyone who challenges his narrative of events—including pertaining to Habyarimana’s assassination—as a genocide denier.

According to J.E. Murphy, a former RPF intelligence officer writing under a pseudonym, the assassination [of Habyarimana] bore the signature of Bill Clinton, the U.S. President.

“Clinton wanted Habyarimana killed for Kagame to take over the country [Rwanda] no matter what cost. Important for Clinton was to get Mobutu out of Congo using Kagame and Museveni to carry out their mission. Several American corporations were interested with Congolese minerals, and the president had to enable them to get their piece of pie, and the only obstacle to that business was Mobutu, the dictator in Kinshasa who once was the cherished boy of [the] United States.”

Kagame lived up to his potential when he twice invaded Congo and imposed a quisling ruler (Hyppolite Kanambe a.k.a. Joseph Kabila), who opened Congo to foreign exploitation.

Source: whale.to


Millions of Congolese were killed as Western corporations such as American Mineral Fields (AMF), headquartered in Hope, Arkansas (Bill Clinton’s hometown), and Barrick Gold, on whose board sat George H.W. Bush and ex-Canadian Prime Minister Brian Mulroney, received concessions for mining mineral resources worth more than $157 billion.

Barriers to Prosecution

The geopolitical backdrop and huge profits helps to explain Kagame’s immunity from prosecution—despite the strong evidence implicating him in one of the great crimes of the late 20th century.

A January 2000 article in the Canadian National Post reported that Louise Arbour, the chief prosecutor for the International Criminal Tribunal for Rwanda (ICTR), had terminated an investigation into the shootdown of Habyarimana’s plane after three Tutsi informants came forward in 1997 with detailed accusations against Kagame and the RPF.

They claimed that they had been members of an “elite strike team” responsible for the downing. 

Following the National Post’s article, a three-page memorandum written by investigator Michael Hourigan was sent to the ICTR where defense attorneys had requested it. 

Hourigan stated that investigation into the shootdown of Habyarimana’s plane was clearly within his mandate and that he was “astounded” when Arbour made an about-face and told him it was not.

This sequence of events was confirmed by Hourigan’s boss, Jim Lyons, the former FBI agent who headed the so-called National Investigative Team.

Lyons believed Arbour was acting on orders to shut down the investigation. Arbour’s predecessor Carla Del Ponte had been fired when she too had pressed for it.

In April 2010, when Kagame was slapped with a $350 million wrongful death lawsuit by the widows of Habyarimana and Cyprien Ntarimana while visiting Oklahoma to give a commencement address, the Obama administration filed a Suggestion of Immunity on Kagame’s behalf, making it difficult to prosecute him.

In France, the Bruguière investigation implicating Kagame in Habyarimana’s assassination was smothered by the political realignment in France prompted by the election in 2007 of Nicholas Sarkozy, who sought better relations with the U.S., and the appointment of Bernard Kouchner as French Foreign Minister.

François Hollande also pursued the same policy of his predecessor, as has Emmanuel Macron who visitited Kigali during the commemoration of the genocide in 2021.

Editor's Note:

This article was first published on the CovertAction Magazine and has been posted here under its cross-posting terms.