He subsequently opened the gates of the hospital compound to people seeking a place to sleep that was safe from rebel attacks and abduction.
In a later incident, Lukwiya, his wife Margaret and five children were lying in bed one evening listening to nearby fighting between the rebels and government forces when a mortar shell crashed through the ceiling of their house, but failed to explode.
Under Lukwiya's administration the hospital tripled its capacity to 18,000 patients annually, included wounded from both sides of the conflict, and a further 500 out-patients daily.
There he sought a master's in public health at Makerere University, leaving the running of the hospital to colleague Cyprian Opira.
[1] On the morning of 7 October 2000, Lukwiya received a phone call from Opira informing him that a mysterious illness had killed two of the hospital's student nurses, all of whom had begun bleeding or vomiting blood.
Opira asked Lukwiya for help and he arrived that evening, in time to witness the death of a third nursing student, Daniel Ayella.
He had head nurse Sister Maria Di Santo bring him the charts of all unusual deaths in the past two weeks and identified 17 cases with similar symptoms.
Lukwiya immediately recognised this as a particular problem in Acholiland, where the traditional practice was for the bereaved family to wash the body of the deceased before burial.
By the time the team arrived, Lukwiya had already set up an isolation ward for suspected Ebola cases, in line with the WHO guidelines.
[1] When a South African lab confirmed the Ebola outbreak on 15 October, and a WHO delegation arrived in Gulu, they were astonished at the efficiency of the operation.
I thought we would be facing a situation where patients were totally neglected and an isolation ward to which people wouldn't want to come because it would just be a mortuary But they had implemented the manual – a very specialized recipe.
However, despite instituting risk minimisation procedures, including wearing of robes, multiple gloves, surgical masks and goggles, hospital workers continued to fall ill. Twelve more died.
The day-shift did not go to work; instead 400 health workers, nearly the entire staff of St. Mary's, gathered in the assembly hall of the nursing school.
After hours of contentious discussion that extended into the afternoon, Lukwiya switched back to a conciliatory approach, stating that he would remain no matter if everyone left.
[1] After finishing his days in the isolation ward, Lukwiya would sit with members of the WHO, CDC and other medical teams that had set up in the hospital compound to offer assistance and take blood samples that allowed them to map the course of the disease.
Health workers at St. Mary's worked 14 hours shifts for weeks in a row while in layers of protective clothing that were stifling in the equatorial country.
All that would be required for infection is for a health worker to lose focus for a moment and, after touching a patient, slip a gloved finger under their mask to scratch an itchy nose or rub an eye.
Fighting to breathe, Ajok pulled off his oxygen mask and coughed violently, sending a fine spray of blood and mucus against the nearby wall.
[1] On the evening of Sunday, 26 November, two days after he had convinced the nurses to remain on the job, Margaret was startled to hear her husband's voice sound heavily congested.
His fever grew worse through the day, a Monday, and by Wednesday was vomiting and Dr. Pierre Rollin of the CDC took blood samples for testing.
A nurse who was administering an intravenous drip that evening at his home was surprised when he began speaking distinctly, though not to her: "Oh, God, I think I will die in my service.
Among the hundreds of mourners who were warned to stay back until the burial was complete were Lukwiya's children and numerous government officials, including the Minister of Health, who had rushed from Kampala after receiving word that morning.
Foreign epidemiologists credit Lukwiya with accelerating the government's public education campaign to stop the spread of the disease with his phone call to Kampala on 8 October.