During a period of military dictatorship supporting the Salvadoran elite, he and his fellow Jesuits taught peasant communities to stand up for their rights.
The government's response was a "scorched earth" campaign against the peasant population, deemed either to be terrorists or their supporters, with widespread massacres of civilians, even children.
When a fellow Jesuit, Rutilio Grande was murdered by government forces in 1977 while returning to his parish church in Aguilares, Archbishop Óscar Romero (who was himself assassinated in 1980) appointed Cortina to succeed him as the pastor of the village.
While driving back to the capital the next day, he heard on his car radio the news that all occupants of the Jesuit resident at the university had been executed overnight by a large contingent of government soldiers.
[1] After the civil war came to an end in 1992, Cortina began to hear reports from refugees that many children were unaccounted for, their bodies not being among those slain in the massacres.
He also heard rumors from soldiers that some of the children from these villages had been taken and later "sold" to childless couples from the United States and Europe who were looking to adopt.