On December 7, 1975, troops from the Republic of Indonesia initiate a formal invasion of Timor-Leste. Thousands of paratroopers descend over Dili, and dozens of landing barges attack its shores. The carnage is immense. At the bishop's residence, D. José Joaquim Ribeiro and his vicar-general, Martinho da Costa Lopes, are alerted to the ongoing massacre. Later on, the latter would recall that day:

Full occupation of the territory would take several years. As the Indonesians progressed and the number of victims skyrocketed, the Catholic Church was increasingly asked to perform a task many would not anticipate. During the whole period of occupation – that is, up to 1999 – an estimated one-third of the population perished in dire circumstances. Priests and nuns will denounce, both internally and externally, using the network of the Church, the widespread violation of human rights. Many of them will help, counsel and cooperate in active ways with the Timorese Resistance. Some priests joined the guerrilla fighters in the mountains, exercising their religious munus with them, and eventually discharging political functions. In the so-called Clandestine Front, formed by many civilians, several clergymen assumed a position in the organisation. Many were the ways in which the Timorese Catholic Church became involved with its people's struggle for independence.