When the guns fell silent in northern Uganda in 2005 after two decades of the Joseph Kony-led Lord’s Resistance Army (LRA) insurgency, survivors expected a speedy return not just to a normal life but to prosperity as well.

The Uganda government, thanks to donors’ largesse, kicked to life a Ush1.1 trillion ($426 million) rehabilitation programme baptised Peace, Recovery and Development Plan (PRDP) to fast-track the region’s re-emergence from the ravages of war. It focused on big ticket investments: Infrastructure development, rebuilding collapsed government institutions and opening rural roads as well as communal farmlands.

Things, however, turned topsy-turvy. Bureaucrats at the Prime Minister’s office allegedly filched $13 million from the PRDP account, prompting the development partners in December 2012 to withhold $300 million in approved aid. The resultant delay in the implementation of earmarked development projects dimmed the region’s hope of getting out of poverty.

READ: Relief efforts in Uganda at stake as donor commitment declines

And as if that was not enough, a more sinister monster kept coursing the path of LRA’s atrocious war: Sexual and physical assault on women, mostly single mothers.

Unlike the mortar blitz that caught national and international news headlines, this nascent gender-based violence is under-reported, and the victims face their plight as personal tragedy.

In the pre-insurgency period, a dignified man in northern Uganda earned respect by providing for his household, safeguarding both his wife and children and accumulating wealth. Today, brutality has replaced that virtue in most rural areas where LRA operated.

In the week of September 21-26, 2013, a police officer in Gulu district was beheaded for allegedly being caught red-handed in bed with another man’s wife.

At Keyo PS, about 5km out of Gulu town, six girls – two in Primary Six and four in Primary Seven – were defiled several times by their teachers and got pregnant. They eloped. One of the girls is reportedly six-months pregnant and only two returned to school for the final term on the school calendar which ended December 2013.

The rest are in hiding and therefore will not even benefit from ante-natal and prevention of mother-to-child HIV transmission (PMTCT) services available at the health facilities.

Police are investigating allegations that at the neighbouring Keyo Secondary School, teachers impregnated three girls. One teacher has been remanded while his colleagues went scot-free after paying bride wealth to relatives of the girls.

According to police records, 585 girls were defiled and 55 women raped between January and September 2013. Residents say many such cases — perhaps the majority — go unreported to authorities.

Sexual abuse and physical assault are men’s new “weapons to ‘discipline’ women,” says Judith Pamela Angwech, the executive director of Gulu Women’s Economic Development and Globalisation (GWED-G).

The organisation, which has more than 20,000 members clustered in 78 village groups, rehabilitates and assists victims of gender-based violence, and runs a self- help scheme under which women save money for a rainy day.

Ms Angwech attributes the abusive trend to the war. On September 23, 2013, GWED-G received a 19-year-old girl who was two-months pregnant and who had been raped by her brother-in-law. She had to undergo emergency surgery at Gulu Independent Hospital.

“People learnt abusive ways from the war,” Ms Angwech said. “Rebels and government soldiers raped women, and men who have become frustrated do it as a way of life.”

At the height of the LRA insurgency, the government forced the affected communities into camps, where an estimated 1.7 million people lived in squalor, on hand-outs and without privacy. The rebels often attacked the IDP camps, raping women and killing people in the open. People’s cultures were defiled.

The camp life left generations of young men and women without cultural decorum. They grew into adults alien to their community’s ways of life.

The brutal wars in the region pitted LRA rebels against government soldiers and it saw thousands of women abused. They were subjected to sexual slavery, physical assault and forced marriages. Many were also physically disfigured, with some losing their lips or ears.

As a result of these violations, many victims developed reproductive health complications that have significantly impinged their ability to settle into a productive life after the war.

Formerly abducted women who have returned home continue to face sexual abuse. Rose*, for instance, was abducted when she was barely a teenager. She spent close to 10 years in captivity but escaped together with her husband, a rebel commander she was forcibly married off to and who is still with her.

Since 2010, Rose has endured abuse from the man who first raped her nine years ago. The husband has punched out five of her upper front teeth and her body is scarred from the man’s constant beatings.

“He even rapes her in the presence of her children,” said Ms Jolly Okot, the co-founder of Invisible Children, a local NGO.

The victim, who has no skills or means of alternative livelihood, worries that she would be worse off if she abandoned her tormentor. Like many youthful women in northern Uganda, Rose’s hardship is compounded by the fact that she has no formal education.

Medical reports by organisations such as Isis-WICCE, the US-based cross-cultural organisation, show that many women in former conflict areas suffer loose and prolapsed uterus either as a result of many births that were not properly spaced out or because of repeated rape and lack of immediate medical attention.

In the organisation’s assessment, most of the women need surgical procedures, which they can’t afford.

Economic recovery in 16 districts in the sub-region, which bore the biggest brunt of LRA war, has further been slowed by a social epidemic of families headed by single mothers or children.

Several studies by both government and NGOs indicate that the unemployment level in northern Uganda stands at about 60 per cent, twice the national figures.

The Invisible Children currently trains 1,000 girls in various life skills at the organisation’s centre in Gulu district. Ms Okot, 45, says LRA, initially the Holy Spirit Movement, a rebel group then led by Alice Auma Lakwena who claimed to possess mystical powers that could melt bullets, arrived in their area when she was 13 and she was captured.

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President Yoweri Museveni’s government defeated Lakwena’s advancing forces, and her cousin Joseph Kony, a primary school dropout and former altar boy, reorganised the insurgents into what became the LRA rebellion.

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In the bush, she was handed over to a commander as a reward for his fighting prowess. She later escaped. But she says the NRA (the Ugandan military, renamed in 2005 as the UPDF) used to conduct operations in the area and many women were raped.

Ms Okot who grew up with LRA leader Joseph Kony in Odeke village said the rebels use sex as a weapon of war and also a way of punishment.

“Whenever they took us to the garden and we failed to dig, the supervisor would say ‘I will have sex with you tonight to teach you a lesson.’”

But LRA spokesman Godfrey Ayoo and the army spokesman Lt Col Paddy Ankunda both deny that either side was involved in systematic rape of women.

“As far as my understanding of the scientific definition of sex or rape as weapon of war [is concerned], I have not seen any documented evidence nor verbal confirmation of the existence of a policy by LRA to use sex and/or rape as a weapon of war,” Mr Ayoo said.

He instead blamed UPDF soldiers over the reported sexual assaults, an allegation Lt Col Ankunda confuted, pointing an accusing finger back at the rebels.

“If there were such cases [masterminded by the Ugandan military], I am sure they were handled,” he said. “I cannot recall any incident of rape. We would not have condoned impunity when we needed people’s support.”

Sexual abuse occurred, according to victims on a violent and mass scale, but no one now wants to take responsibility.

Alice, 39, who returned home from captivity at the rank of a captain had three children.

Years after escaping from the bush, she married a man who turned out a violent drug addict. Alice, who lives in a crowded Gulu town suburb, where she sells charcoal and foodstuff, has a bullet lodged to her chest and she has no money for surgery.

Yet men keep taking the little she has. “They come and take my things without paying.”

There are stories of former female LRA abductees and their children being rejected by relatives and communities. Whereas the government offered huge perks to surrendering senior LRA commanders, and invested heavily in their re-settlement, ordinary rebel fighters and captives received a few iron sheets and $58 to start businesses.

Thousands became burdens to even the most hospitable host families because they either were physically impaired and therefore unproductive or suffered random psychological trauma.

Many struggle to cope as outcasts. Florence Ayot was born in the capital, Kampala, but the LRA abducted her at 13 years on her maiden upcountry trip and the cousin who accompanied her was killed.

She returned from the bush in 2006, but her relatives said she was “a killer” and unwelcome.

“I wish I had even died in the bush... I find life so difficult,” said the 33-year-old mother of two. “I don’t know how my children’s future will be without me.”

Vast tracts of land here remain idle, and the men who should plough the fertile gardens –fallowed over the 20 years of insurgency — while away their time drinking cheap liquor.

Conflicts over land are escalating. Some returnees found rich and powerful people had grabbed their ancestral lands while many born in the camps could not identify their land. Establishing boundaries on un-surveyed land is difficult, setting neighbours against each other.

And women have been caught up in the crossfire.

Margaret Achayo from Amuru district said her in-laws kicked her out a week after the death of her husband in 2012. She went to her uncle’s home and she has to travel 22 kilometres to cultivate the plots owned by her late husband, which she only accessed after the intervention by ActionAid, an international NGO.

Her plight epitomises vulnerabilities of hundreds of single mothers, widows, child-headed families and former abductees in areas affected by the LRA insurgency.

According to local customs, land belongs to men and they decide what it is to be used for. Local leaders are usually reluctant to protect widows thrown out of their either ancestral land or that of their spouses. A woman must have children to access and use land exclusively to produce food for subsistence.

The PRDP scheme that the government initiated a few years ago is like the elephant in the room, and offers no solution to individual problems.

Mary Karooro Okurut, the Minister of Gender, says the problem cannot be solved by the government alone.

Women who fall victim to gender-based violence face double tragedy: There is a thin police presence, especially in rural communities, with some officers cited as perpetrators, and corruption within the judiciary makes justice a mirage for victims. The abused women therefore come together and share their experiences. In other words, they have become their own counsellors.

But the cycle of poverty and neglect continues.

“If they survive giving birth, the child dies due to lack of proper care or if it is the mother, the child remains destitute,” said Ms Angwech.

Some of the abused girls contract HIV/Aids, and those that become aware of their status abandon the children with their impoverished grandparents and go into prostitution in towns.

HIV prevalence in the north region, comprising the seven districts most brutalised by the LRA war, is at 8.3 per cent, higher than the national 7.3 per cent average, according to the 2011 Uganda Aids Indicator Survey.

Prostitution and illiteracy rates are correspondingly high, and a 2011 Uganda Demographic and Health Survey in the region found that some people in the Acholi sub-region still believe HIV/Aids can be transmitted by mosquito bites or sharing food with an infected person.