But her old friends who had broken free of the rebel group had been heard on the radio, talking about their new lives back in their old villages and urging her to come home.
In the end, she stayed, nursing her nine-month-old son until the army arrived and took her to a camp for rescued soldiers in Gulu, northern Uganda.
"When they caught me, I kept waiting for the bullet that would kill me but I am still alive," she said. "I don't know what will happen to me now, but I think I am happy." Lillian's rescue is the result of an attack-and-rescue strategy by Ugandan forces to rein in the Lord's Resistance Army, which has terrorised northern Uganda and neighbouring south Sudan for the past 19 years.
A self-styled pseudo religious prophet, Kony has abducted more than 20,000 children and forced them to kill their own siblings or parents. Girls are raped and given as "wives" to the senior commanders. As a result, the abductees are too ashamed to return home and resign themselves to life with the LRA.
Lillian herself was abducted from her village when she was just 10, taken to the LRA's training camps and forced to work as a domestic servant. Shortly after she reached puberty, Kony chose her to be one of his many wives.
"I had to adapt - I was so little I had no idea what was happening," she said in a near whisper. "I didn't like being his wife, but I always had food so maybe I am lucky. I don't know."
After years of trying unsuccessfully to defeat the LRA through military means, Ugandans are now persuading the fighters to give themselves up voluntarily through a five-year amnesty. Two radio stations, Mega FM and Radio Wa, broadcast programmes in which former LRA fighters urge their friends to come home without fear of prosecution. The messages persuaded hundreds of LRA fighters to surrender, or at least to not resist capture if they are attacked by the Ugandan army.
The broadcasts have proved so powerful that Kony has now banned all but the most senior commanders from listening to the radio, but the message still filters through to the more junior fighters.
Kenneth Banya, who had been Kony's chief military adviser until he was captured a year ago, had made sure he told as many of the young fighters as he could about the messages.
"I had heard former commanders on the radio say they had been welcomed home and these men are not liars, so I trusted them," he said. "It was dangerous for us to tell the younger ones about the messages but we did, quietly, in secret." The Ugandan government believes that the LRA has now shrunk from a force of more than 3,000 to fewer than 300 fighters still hiding out in south Sudan. The support it used to receive from the Sudanese military has dried up and the group is short of food and arms. The army had hoped to capture Kony himself in last week's raid where Lillian Atong was rescued, but he escaped by wading through a river. Nonetheless, Uganda's minister for defence, Amama Mbabzi, told The Independent the noose was closing in around him. "Kony keeps his 'wives', or rather the sex slaves he abducted as children, under extra protection, so if we can reach them, we know that he is weakened," he said. "It is only a matter of time until we get to him."
The government is now so confident that Kony can be captured militarily that it is passing a parliamentary bill that excludes Kony and his five closest commanders from the general amnesty that has persuaded so many of the LRA to surrender. The bill, when passed, will be an admission that Kony is unlikely to be persuaded to lay down his guns voluntarily.
"Right now, the LRA is at its lowest ebb," said Colonel Nathan Mugisha, at the Ugandan army base in Gulu. "He has no support in Sudan and none in Uganda. He cannot go on for much longer and we have nothing more to say to him. When he is alone and friendless, we will get him."
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