Sakure is on the front line of a war that is not supposed to exist. Perched on the rim of the Congo basin, it looks out from South Sudan and into the vastness of the rainforest beyond. The victims of this war are strewn over the floor of that forest, their bodies left to rot, while others have been left as ashes in the charred remains of their villages. Those that have survived are huddled among Sakure's grass huts nervously eyeing the border with the Democratic Republic of Congo across which they fled.

It is a war that is waged by heavily armed soldiers against unarmed villagers and its casualties both living and dead mark the rebirth of Africa's most feared guerrilla group – the Lord's Resistance Army. It was supposed to be a moribund force, a Ugandan rebellion which lost its support and its way after two decades of increasingly sickening violence, with seemingly little point.

A campaign launched in the 1980s claiming to defend the rights of the Acholi people in northern Uganda had become a byword for sadism. Years of abductions where children were forced to kill their own parents in a brutal initiation had left them feared but hated. Their leader and self-styled messiah Joseph Kony was supposed to be on the point of surrender, with his diminishing band of fighters contained in a transit camp awaiting the signing of a peace plan.

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Instead the terror has been transplanted, this time to the remote north of Congo. The bewildered victims of this campaign know nothing of the cause espoused by those that are hunting them – they have never been to neighbouring Uganda. The rebel fighters moved into camps in Congo's Garamba National Park in what was hoped would be the final staging post before peace. But those talks have collapsed after the International Criminal Court issued a warrant for Kony's arrest. A deadline for the end of this month has been given to the guerrillas. They sign the deal or face the consequences, but in their hundreds they have already slipped the net.

All along the border with South Sudan scores of refugees are streaming out of the bush and across the border every day with horrifying accounts of the return of the LRA.

Father Paul was on his way for an afternoon nap on 17 September in the Komboni mission in the Congolese village of Duru when he heard shouting. Looking outside he saw dozens of soldiers marching towards the mission. "They were dressed like soldiers but they were dirty. Some wore witch doctors' hats and dreads in their hair." Marching with them were the girls and boys of the village, women with babies, all carrying their meagre possessions: mattresses, radios, sugar, mobile phones and soap.

Pushing past Father Paul into the courtyard of the mission everyone was ordered to sit on the floor, while the building was ransacked. A frail man in his late 70s, Father Paul was taken to his room and tortured by soldiers who insisted the priests must have money in the mission. "I thought I was going to die so I got on my knees and prayed to the Lord. When they heard me say his name they screamed at me, 'Don't say that word!' And then hit me with their guns."

Such attacks have been replayed across an entire region in recent weeks driving tens of thousands of the Zande people to flee into South Sudan or deeper into the forests of Congo.

The scene, says Father Paul, was straight out of the days of slavery. The children were divided, then bound together and made to march, he remembers.

Left by his attackers in the bush, the priest returned to Duru to see its thousands of shelters ablaze, with the village's only permanent structure, the mission, black and charred. Not a shot had been fired. The group prefer to use machetes. Father Galdino Sakondo, a Catholic priest who has been working with victims of the terror on both sides of the border says the silent tactic is deliberate. "They don't shoot, they are just chopping. You don't know they are there until they reach your house."

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That was the fate of 15-year-old Neima Kumbari in the village of Napopo. "They came in the morning but I didn't see them at first." When she did realise the soldiers had arrived it was already too late. Her parents were beaten with rifle butts, then, along with her uncle and a brother, burned alive in their own hut. The soldiers had "no mercy", she says.

Neima escaped by running into the bush while her village was torched, stepping over the fallen bodies of her dead neighbours as she ran. After two days she reached Sakure having lost everything, her whole family. In a flat, calm voice, Neima says she is still haunted by the bodies she stepped on.

Philip Charles didn't get the chance to run. A shy, quiet 16-year-old, he was at home near the Congo border when the area was overrun by a raiding party from the LRA. The children were abducted, their families' looted possessions strapped to them and then they were tied together in pairs and made to sit in silence. "If we made a sound they would beat us to death," he was told.

Later after the LRA fighters had been repelled in an attempted attack on Sakure they frog-marched "many" children into the forest.

Philip remembers telling the girl he was tied to that they had to find a way to escape. "I was thinking I wouldn't survive. They wanted to turn us into soldiers." After a night in captivity he was able to untie himself, throw down his heavy load and run into the bush. She was not so lucky. The fate of the lost girl is as predictable as it is nightmarish.

Amony Evelyn was 12 when she was taken under similar circumstances. Her life in the bush was a mixture of drudgery and torture. Part cook, part porter, part sex slave to Joseph Kony himself. A man many believe to be clinically insane, he is said to see his mission as "purifying" the Acholi people and to encourage a quasi-religious cult involving black magic. She bore him two children, the first when she was still 13 and was pregnant with a third when she fled last year after 10 years in captivity.

Today she is piecing her life back together with the help of a counsellor, Paul Rubangakena from the Catholic charity Caritas, in Gulu, across the border in Uganda. He says the girls and boys in his care "wake up screaming from their nightmares" – even the staff are traumatised by the litany of horrors they have had to hear. The UK-based arm of Caritas, Cafod, is also among the groups assisting the refugees in South Sudan. Raphael Wamae, the group's humanitarian officer, has been part of an early assessment team who arrived on the scene to gauge the scale of the refugee crisis. "We cannot ignore what is happening here because of events in Goma. This is part of the same crisis. Armed factions are roaming Congo preying on defenceless people," he says.

Already more than 5,000 refugees have been counted, all in desperate need of food and shelter. Countless more are roaming the bush and some 60 more are arriving every day. Catholic church groups are calling for urgent assistance and warning that the area risks being ignored.

"The same factors driving the humanitarian disaster in Eastern Congo are at play here: weak states, lack of law and order and the scale of mineral wealth in DRC leave ordinary people at the mercy of men with guns," says Mr Wamae.

Just as in the crisis in the east of Congo, the national army does nothing to protect its people and the UN peacekeepers, Monuc, are powerless to help.

At stake are a mesh of competing interests that stretch from Khartoum, through Darfur to the threatened Eastern Congolese city of Goma and the capital of Rwanda, Kigali. Rebel groups can be used to control the money generated by Congo's fabulous mineral wealth but they also serve the dual purpose of helping to destabilise regional rivals. A recipe for proxy wars without end.

Lexon Bashir, the director of the South Sudan Relief and Rehabilitation Committee, rails against the "so-called LRA". "Why are they abducting children? Sudanese boys and girls as well. We have seen children burnt beyond recognition their bodies thrown into fires." He sees an outside hand in the violent re-emergence of Mr Kony's cult but refuses to say whose.

In private others are less reticent, pointing to helicopter drops of arms and ammunition to the LRA. They believe that the government of Khartoum led by President Omar al-Bashir – a fellow indictee the ICC – is helping Kony's army with a view to destabilising southern Sudan ahead of a possible resumption of that civil war.

In the clearing of Sakure, thousands of miles from Khartoum, girls like Neima suffer the reality of these machinations. Despite nearly 400 soldiers from South Sudan stationed here to protect them and UN food aid finally reaching the refugees, she feels that she is still being hunted. "There is a war," she says. "I don't know what they want but I have heard they are called the LRA. I'm scared. They are coming to Sakure."

The altar boy who became a rebel leader who turned into a psychopath. The self-styled prophet Joseph Kony has remained an elusive and terrifying figure casting a spell over first Uganda, then Sudan and the Central African Republic, and now the Democratic Republic of Congo.

Born in 1961, he inherited his mantle as leader of the Acholi people from his aunt, Alice Lakwena, a mystic who started the Holy Spirit Movement against the government in Kampala.

While initially enjoying strong public support, Kony's group, the Lord's Resistance Army, turned on its own supporters in an increasingly brutal and incoherent campaign, supposedly bent on "purifying" the Acholi people and turning Uganda into a theocracy ruled by the Ten Commandments.

His army has been forcibly recruited from the Acholi, with as many as 20,000 children abducted and forced to commit atrocities that prevented them from returning home.

He has nurtured a cult of personality, claiming he is visited by a multinational host of 13 spirits, including a Chinese phantom. Former abductees speak in awed terms of his "magical powers" and abrupt mood changes. He is said to have taken up to 60 wives and fathered countless children.

A school dropout described as a "gentle boy" by classmates, he has become one of the most sadistic leaders in Africa. In 2005, the International Criminal Court issued a warrant for his arrest for crimes against humanity.