There will probably never be agreement as to what led to what, but a common view is that rogue NRA units took to arresting and even killing ex-military men from the region, and persecuting old regime supporters.
The north rose in arms, first through the Uganda People’s Democratic Movement/Army – which eventually cut a peace deal with Kampala in 1988.
Then, most famously, there arose the Holy Spirit movement, led by a former prostitute turned spirit medium, Alice Auma.
Because the spirit she channelled was called Lakwena, she became known as Alice Lakwena.
Lakwena’s Holy Spirit was a millennial movement whose rise is traceable many decades back before Lakwena led it to take up arms against the new Museveni government.
But the immediate spark was the threat and harassment by the new victors, and Lakwena’s understanding that northerners, especially the Acholi, were in a deep crisis and demoralised.
Lakwena figured that having been failed by mortals, she could only mobilise the north by appealing to heavenly forces.
She came up with the idea that the people who joined her struggle would be the Holy Spirit’s soldiers, and He would protect them with greater powers.
Thus if they smeared “miracle” shea butter oil on their bodies, the bullets of Museveni’s soldiers would not kill them. Many believed it.
In fact, Prof Isaac Newton Ojok, who was minister of education in the Obote government that was overthrown in 1985, was one of several highly educated people who threw away their designer shirts and followed Lakwena, barefoot, on her spectacular but ultimately tragic march on Kampala.
The Museveni rebels had succeeded by clever and asymmetrical guerrilla warfare.
Therefore little in their five-year war, where preserving their numbers were critical, prepared them for an adversary who didn’t fear death or take cover in the face of heavy fire.
The fact that Lakwena was able to raise a large highly motivated army that was not afraid of bullets, and because the slaughter of Holy Spirit fighters unnerved the NRA, allowed her to make the greatest advances ever against the Museveni regime of all his many enemies.
By November of 1987, Lakwena was massing in the sugarcane plantations outside the industrial town of Jinja, less than 90 kilometres from Kampala.
In the capital, some Museveni regime supporters panicked. A few hightailed it out of Uganda back to Europe and North America, while some took the milder precaution of shipping their families out.
That threat galvanised the Museveni government, and in a ruthless fightback, obliterated the Holy Spirit movement in the sugar plantations of Kakira.
In November 1987, Lakwena fled to exile in Kenya, where she died in a refugee camp in 2007.