Thirty minutes later he was dead, his bullet-riddled body dumped on the muddy banks of a creek less than 100 meters from his modest two-bedroom home in Malobago, a quiet, impoverished farming village in the eastern Bicol region.
Sta. Rosa’s case got little attention in the national press, his death only a statistic added to the more than 700 activists gunned down by so-called paramilitary "death squads" in the Philippines in the past five years alone.
But what made this case different was that it offers the first real hard evidence that the military was involved in the killings: one of the abductors was accidentally killed in the burst of gunfire that also felled Sta. Rosa.
An ID card in the gunman’s pocket identified him as Lordger Pastrana, a member of the army’s intelligence group who was out on a "secret mission" to liquidate leftist dissidents.
The circumstances surrounding Pastrana’s death remain cloudy, but it appears he was accidentally shot by his own men in the confusion. There was a clumsy attempt at a cover-up, with police saying the soldier only happened to pass by after visiting a girl he was courting.
But they could not explain why he ended up lying dead on the creek bank beside the pastor.
"The street lights were put out and there were heavy footsteps in the rice field. They stormed the house and pointed guns at us, including my four children. They hogtied Isaias and were forcing him to confess that he was a communist rebel," Sta. Rosa’s widow, Sonia, told AFP, her steely resolve giving way to sobs.
"He was isolated in one bedroom and we could hear muffled cries of anguish. He was being tortured, there was blood on the floor. I remember Pastrana telling us to cooperate and we will not be harmed," she said.
"My husband was then taken out and there was a burst of gunfire. Minutes later, we found his lifeless body and near him was the dead soldier," she said.
"My children are now fatherless and in shock."
How Sta. Rosa could be mistaken for an insurgent is not exactly clear to Sonia, who met the mild mannered pastor in the 1980s when he first arrived here to head a chapel.
The pastor would later devote his time to organizing grain funding programs for farmers, gaining the respect of the community. In a local gazette, he wrote scathing remarks about some of the policies of President Gloria Arroyo, but he never espoused violence or armed struggle.
"He has never held a gun in his life. His pen was his weapon. True, he may have railed against policies of the Arroyo government, but who hasn’t? That does not make him a rebel targeted for killing," she said.
A report by the Commission on Human Rights after a fact finding mission, which was obtained by AFP, said there is "legal ground" to prosecute Pastrana’s commanding officers for the incident.
So far, a special commission created by Arroyo to investigate political killings has not interviewed the widow or other survivors.
None of Pastrana’s superiors were available for comment, but a senior military officer in the region said military intelligence were known to monitor "groups of interest" – a euphemism for those they suspect as fronting for the communist New People’s Army (NPA), which has been waging a Maoist insurgency since 1969.
"These groups are being monitored. But the military does not employ death squads," he said, though he conceded there could be elements within the military carrying out their own "special operations."
The Army command post here sits on a hillock and is constantly under attack by NPA rebels, who are known to have infiltrated many remote hamlets from where they recruit impressionable youths.
"It’s difficult to know for sure who your real enemies are," the official said.
The military headquarters in Manila has officially denied having a hand in the killings, saying those killed so far were victims of an internal purge carried out by the NPA among its own ranks.
But for veteran street parliamentarian Pedro Gonzales, 62, the battle lines are clearly drawn. He says military intelligence units are always on his tail, ready to pounce if he again lets down his guard.
Two years ago, two men pumped nine bullets into the head and body of Gonzales in a ruthless daytime ambush just outside his house in Quezon province south of the capital.
An outspoken critic of Arroyo who has led street protests as leader of the National Fisherfolk Movement, Gonzales was a popular candidate for a provincial board seat in his hometown when he was attacked.
"They waited for me outside my home and shot me at close range. But by a stroke of miracle, I am still alive. I still have some metal lodged in my body and I am in therapy," said Gonzales, who now walks with a limp and a cane after his sense of balance was permanently impaired by the shooting.
"It is clear in my mind – they were military hit men who want me silenced. But I will not give them that satisfaction, I will continue to call for Arroyo’s resignation," he said.
Gonzales still is a fixture in near-daily street protests around Manila, but has not returned to his hometown since the attack. He stays with friends, and often jumps from one bus to another to evade "death squads who stalk me."
"I know, they are just waiting for a chance," he said.
The spate of killings targeting activists has alarmed the European Union, Amnesty International, Human Rights Watch and the Roman Catholic church, all of which have called on Arroyo to take action to stop the killings.
The blood has not stopped flowing.
Amnesty International said in a report in August that "a failure to prosecute any of the killers risk perpetuating a cycle of human rights violations, not least by sending a message of de facto state tolerance for such practices."
"Such a climate of impunity undermines public confidence in the administration of justice, eroding the rule of law and respect for human rights," it said. - AFP