For more than 20 years, Fulgence Kayishema, one of the world’s most wanted fugitives of the Rwandan genocide, evaded authorities who say he orchestrated the killing of more than 2,000 Tutsis during the massacre.

He remained at large, hiding among refugees in several countries, and masking himself behind various aliases.

This week the police finally caught up with him in South Africa.

Mr. Kayishema, 61, was arrested Wednesday on a grape farm outside Cape Town, authorities said. It took a multinational team, including South African police and the United Nations International Criminal Tribunal for Rwanda, casting a wide net to catch him.

Mr. Kayishema has been one of the tribunal’s most wanted fugitives since his indictment in 2001. Unlike the high-level politicians or generals already prosecuted as the masterminds of the 1994 Rwandan genocide, Mr. Kayishema had a direct hand in the killings, according to Serge Brammertz, the tribunal’s chief prosecutor. According to the indictment, Mr. Kayishema was the chief police inspector in 1994, overseeing and participating in the days-long massacre of civilians.

“He was not only organizing and planning, but he was himself involved,” Mr. Brammertz said.

Mr. Kayishema faces multiple charges for genocide and will now be extradited to Tanzania, where he will be tried by the International Criminal Tribunal for Rwanda.

Credit…International Residual Mechanism for Criminal Tribunals, via Associated Press

As the killings began to spread across Rwanda during in April 1994, more than 2,000 women, children and elderly Tutsi civilians sought refuge in Nyange Parish Church in the Kivumu commune, west of the capital, Kigali. The Catholic church was quickly surrounded by Hutu Interahamwe militia. Instead of intervening, police officers aided the killers with Mr. Kayishema at the helm, prosecutors say.

When killing by machete took too long, Mr. Kayishema is believed to have procured gasoline that he and others poured onto the church, before lobbing grenades through the windows, prosecutors said. He and his accomplices drove a bulldozer over the church, crushing any survivors. He then oversaw the digging of mass graves in the church grounds, the charges say.

“He really took advantage of his position to really prepare and commit those massive crimes,” Mr. Brammertz said.

In the aftermath of the genocide, Mr. Kayishema went into hiding, living in camps among the vulnerable and displaced as he manipulated the asylum process across several countries, according to the prosecutors. He fled Rwanda in 1994, crossing with his family into the Democratic Republic of Congo. He then left for neighboring Tanzania, taking on the identity of a Burundian asylum seeker, moving between two camps.

Several years later, he and his family traveled farther down Africa’s east coast, seeking asylum in Mozambique, eventually arriving in the kingdom of Eswatini in 1998. The tiny landlocked kingdom was a springboard to neighboring South Africa, where Mr. Kayishema spent the next two decades building a new life.

To evade authorities, he created several aliases, shuffling passports and visas of at least four identities known to authorities, including a Malawian nationality. It was so effective that he obtained asylum status in two different countries, South Africa and Eswatini, in the same year. At the time of his arrest, he was known as Donatien Nibasunba, a Burundian national.

A network of Rwandan exiles are believed to have facilitated his movements, specifically members of the now-disbanded Rwanda Defense Force and of the Democratic Forces for the Liberation of Rwanda, an armed group accused of atrocities. In Cape Town, Mr. Kayishema worked as a security guard in a shopping mall parking lot. The company he worked for was owned by one of these groups, Mr. Brammertz said.

But this network would also prove his downfall. Investigators used telephone records, financial statements and cross-border travel to narrow their search. By “shaking the tree” of his close associates and persons of interest, authorities were able to track the fugitive to a modest one-room house, where lived as a laborer on a grape farm in Paarl, a small vineyard town outside Cape Town, Mr. Brammertz said.

The operation came together in the last few days after years of what Mr. Brammertz has said was slow response from South Africa and Eswatini.

In one instance, South African authorities said they could not act because Mr. Kayishema had been granted refugee status, according to Mr. Brammertz’s 2020 report to the U.N. Security Council. Another time, Mr. Kayishema’s records simply disappeared.

In the last 10 months, though, South African authorities assigned a 20-person team to the case. They were part of the coalition that tracked and detained him. South African police officials say the fugitive will face charges for breaking South Africa’s immigration laws.

Mr. Kayishema was one of several men indicted on charges linked to the massacre. Others have been captured, while at least two are believed to have died. The church’s priest, Athanase Seromba, is serving a life sentence for his role in the massacre, while a pharmacist named Gaspard Kanyarukiga is serving 30 years. Félicien Kabuga, a wealthy businessman who had been on the run for 23 years, has been on trial since last year. Mr. Kabuga is charged with inciting genocide through his radio station while also providing weapons and financial support to the Interahamwe militias.

“It is very likely that this is the last big arrest of a fugitive by us,” Mr. Brammertz said.

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