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United Nations peace keepers record details of weapons recovered from Democratic Forces for the Liberation of Rwanda (FDLR) militants after their surrender last year.Kenny Katombe/Reuters

It could be the final chapter of the wars that began with the Rwandan genocide. Sometime soon, perhaps within days, a military coalition will plunge into the Congolese bush to pursue the last of the génocidaires.

Twenty years after the genocide that killed an estimated 800,000 people, some of its perpetrators are still a deadly threat. They are among the leaders of a brutal rebel militia known as the FDLR in the east of the Democratic Republic of the Congo, where they fled across the border from Rwanda after the genocide. But now a coalition of troops, mostly South African and Congolese, is mobilizing to hunt them down.

With wars already killing thousands in Nigeria, Somalia, South Sudan and the Central African Republic, another war might seem like the last thing Africa needs. But this one, if done properly, could help to stabilize one of the most violent regions of the continent, where millions have died since the 1994 genocide.

Doing it properly will be a huge challenge. The FDLR – known in English as the Democratic Forces for the Liberation of Rwanda – are intermingled with the civilian population in a remote and impoverished area, protected by nearly impenetrable jungle and marshes. They have shown a willingness to massacre villagers to deter attacks and put pressure on the international community. A previous bungled attempt to wage war against the FDLR, by an international coalition in 2009, forced nearly a million people to flee their homes.

The génocidaires themselves are only a small minority of the FDLR's commanders by now. But the ethnic Hutu militia is factionalized and divided into small units that will simply scatter in the bush or blend into the civilian population when the attacks begin. The FDLR's commanders, fearing imprisonment in Rwanda, are highly unlikely to surrender to the United Nations and Congolese forces that lead the coalition.

Military action has already been postponed twice over the past year, to allow more time for the FDLR to fulfill its repeated pledges to disarm. The latest deadline expired on Jan. 2, and less than 350 of the militia's combatants – just 24 per cent of its estimated total strength – have surrendered in the past eight months, with only 234 of their weapons, according to South African President Jacob Zuma, whose forces are among the biggest in the UN intervention brigade that will do most of the fighting against the FDLR.

Mr. Zuma and other African leaders now say that military action against the FDLR is "inevitable." Headlines in the South African media on Tuesday proclaimed that the South African troops are on the verge of a "major battle" against the rebels. The UN Security Council, in a vote last week, called for "robust military action" against the FDLR.

Humanitarian agencies in eastern Congo are preparing for the probability of war, along with likely reprisals against civilians by the rebels. The relief agencies worry that the military operation will displace civilians and disrupt the supply of humanitarian aid to thousands of desperately poor villagers.

Martin Kobler, the UN special envoy to Congo, acknowledges there were "a lot of civilian casualties" in the 2009 operation against the FDLR with "villages burnt, women raped and civilians killed." This must not happen in the new operation, he told reporters in the Rwandan capital, Kigali, this weekend.

"We want to avoid it and we want to mitigate the effect on the civilian population," he said.

"We want to target FDLR combatants. We are not going to target civilians, we are not going to target the Rwandan refugees and we are not going to target the Congolese Hutus who are living in the area."

Rwanda and the United States are pushing hard for military action against the FDLR, with some U.S. sources claiming that the FDLR are using the delays to regroup and rebuild, instead of disarming. But the two biggest troop-contributing countries in the intervention brigade, South Africa and Tanzania, are much less keen on military action. Both have poor relations with the Rwandan government.

South African troops would be crucial to the anti-FDLR operation, as they were in 2013 when they helped defeat the Rwandan-backed M23 rebels in eastern Congo. But in a statement on Jan. 3, Mr. Zuma announced that any action against the FDLR would wait until after a regional summit this month in Angola to discuss and co-ordinate the action.

Critics called this a stalling tactic, and Rwanda denounced it a "waste of time and money." Last week, Angola cancelled the summit, saying that everyone already agreed on the need for military action.