The Ugandan Army is hunting down the rebels of the Lord’s Resistance Army in three African nations.

OBO, Central African Republic — The night is inky, the helicopters are late and Cmdr. Patrick Opiyo Makasi sits near a dying cooking fire on a remote army base, spinning his thoughts into the darkness.

“It was either them or me,” Commander Makasi said of the countless people he has killed. “Them or me.”

The Lord’s Resistance Army, a notoriously brutal rebel group, snatched him from a riverbank when he was 12 years old, more than 20 years ago, and trained him to burn, pillage and slaughter. His name, Makasi, means scissors in Kiswahili, and fellow soldiers said he earned it by shearing off ears and lips.

But now he has a new mission: hunting down his former boss.

In an unorthodox strategy that could help end this seemingly pointless war, the Ugandan Army is deploying special squads of experienced killers to track down the L.R.A.’s leader, Joseph Kony, one of the most wanted men in Africa, who has been on the run for two decades.

These soldiers, like Commander Makasi, are former L.R.A. fighters themselves, and just about all of them were abducted as children. They recently surrendered and are now wading through black rivers and head-high elephant grass across three of the most troubled countries in the world — the Central African Republic, the Democratic Republic of Congo and Sudan — where the last remnants of the L.R.A. are believed to be hiding. They say they know all of Mr. Kony’s tricks.

Some critics may not think this wise, putting so much trust in men whose moral compass had been turned upside down for so long.

But the Ugandan government is desperate to finish this conflict, which ravaged northern Uganda and killed thousands. The government’s policy is to grant amnesty to all L.R.A. fighters except the top three, who have been indicted by the International Criminal Court: Mr. Kony; Okot Odhiambo, his deputy; and Dominic Ongwen, another commander who is widely believed to have planned a massacre in Congo in December in which hundreds of civilians were bludgeoned to death.

The American government considers the L.R.A a regional menace and is helping the Ugandans by providing millions of dollars of military support, namely, trucks, fuel and contracted airplanes.

Some American officials said that they had mixed feelings about the former rebels’ being involved, though they said that the decision was the Ugandans’ and that in this case, as one American officer put it, “these guys may be some of the best they got.”

The battlefield statistics seem to bear this out. In the past 18 months, American officials say, the Ugandan Army has killed or captured more than half of Mr. Kony’s men, including his finance and communications officers, as well as several other high-ranking commanders.

“And let’s be realistic,” added the American officer, who was not authorized to speak for attribution. “These ex-L.R.A. guys don’t have many skills, and it’s going to be hard for them to reintegrate.

“But one thing they are very good at,” the officer said, “is hunting human beings in the woods.”

The woods around Obo are thick, wet and endless. These are the brown and green jungles camouflage was made for. At night, they swallow what little light emanates from the cooking fires flickering on the Ugandan base. The Ugandans find themselves several hundred miles from home, in a country not even bordering theirs, because Mr. Kony has brought them here.

Mr. Kony, a former Catholic altar boy who became possessed by spirits (including one named Who Are You?) and went on to lead a bizarre rebellion with thousands of followers, gravitates to where government is weakest. His movement started in the late 1980s, ostensibly to liberate oppressed Ugandans, when Uganda was just emerging from civil war. As soon as Uganda rallied behind a strong central government, Mr. Kony scurried off to southern Sudan, where the Sudanese government gave him sanctuary.

When a peace plan in the early 2000s brought some stability to southern Sudan, Mr. Kony moved again, marching his fighters, child brides and military-grade weaponry first to eastern Congo, whose lawlessness has drawn dozens of renegade groups, and then to Central African Republic, a vast, scarcely inhabited country where the government is invisible in many parts and the economy so underdeveloped that one of the country’s signature products has become pictures made from insect wings.

In the past few months, the L.R.A. has killed dozens of civilians in remote villages and replenished depleted ranks by kidnapping children — just as it always has. Mr. Kony seems to be circulating between Central African Republic and the Darfur region of Sudan, which is a problem for the Ugandans, because while they have permission from the authorities in Congo, Central African Republic and southern Sudan, they are not allowed to cross into northern Sudan. Recently rescued women who were part of his conscripted harem said that he still had adequate supplies, including a solar-powered television.

“Sometimes he watches movies to cheer himself up,” said one woman, Alice Auma. “Rambo’s his favorite.”

In a way, certain chapters of this conflict have unfolded like a bad script, since so many times, when Mr. Kony and his band of killers have been surrounded in the bush, facing superior firepower, with the credits about to roll, he escapes.

But that may be changing. Every day, dozens of squads of Ugandan soldiers, several thousand in total, suit up at dawn with assault rifles and belt-fed machine guns slung over their backs, rubber Wellington boots pulled up to their shins and their bodies powered by a few scalding cups of tea and some banana porridge.

Commander Makasi, 35, leads one of these squads. The Ugandan officers seem impressed by his professionalism and say that of the several hundred former rebels who have worked for the army, few, if any, have defected. Human rights observers said the Ugandan military had performed admirably in this operation.

“I’m really pleased by their behavior,” said Anneke Van Woudenberg, a researcher for Human Rights Watch. “And they’re doing a hell of a hard job.”

There is the mud and the vines that wrap around legs like bolas and a certain leaf that causes such anguish when brushed against, even through thick clothes, that several Ugandan soldiers had to be airlifted out of the jungle because they dug holes into their flesh by madly scratching themselves.

On top of that, the rebels are savvy bush fighters. Mr. Kony is known to sometimes walk backward to leave misleading footprints or to wade through streams, leaving no tracks at all.

Eventually, though, seasoned hunters like Commander Makasi find a spit-out piece of sugar cane or a depression in the mud where a fighter might have recently slept. Then they close in. A typical skirmish will be a few shots fired by the retreating L.R.A., and a hail of bullets from the Ugandan side.

But Commander Makasi said Mr. Kony was not necessarily fleeing.

“I know this man,” he said. “He’s looking for a place to stay and get strength. He is trying to rebuild.”