Following ordination in 1972, he was assigned to a mission in Bolivia, where the United States was supporting a brutal dictator, General Hugo Banzer. He spoke out against injustice, was arrested, and had to leave Bolivia.
In March 1980, Salvadorian Archbishop Oscar Romero was gunned down while saying Mass. A few months later, three nuns and a lay missionary from the United States were raped and killed by Salvadoran soldiers. Two of the nuns, Maryknoll Sisters, had been his friends.
Shortly after their deaths, he went to to El Salvador where he again found American-trained soldiers brutalizing the people. In November 1989, six Jesuit priests and their housekeeper, with her teenage daughter, were massacred in El Salvador. A Congressional task force later reported that of the 26 soldiers convicted of the murders, 19 trained at the School of the Americas, a U.S. tax-funded military institution run by the Army.
Fr. Bourgeois was given leave by the Maryknolls to study the School of the Americas. He founded an organization called SOA Watch, an independent organization that seeks to close the US Army School of the Americas through vigils and fasts, demonstrations and nonviolent protest, as well as media and legislative work. It has become one of the largest nonviolent resistance movements in America.
Graduates of SOA, he found, include some of the most notorious human rights violators in Latin America, including Bolivia's Banzer, General Manuel Noriega, the former Panamanian dictator and drug dealer now serving 40 years in a U.S. prison, and Robert D'Aubuisson, leader of El Salvador's infamous death squads. The school was teaching torture techniques.
On November 16, 1995, he and 12 others gathered at the main gate of Fort Benning to commemorate the 1989 murders of the six Jesuits and their co-worker and her daughter. After their Mass, they entered Fort Benning and nonviolently re-enacted the massacreand were arrested for criminal trespass, convicted and given sentences ranging from two to six months.