In January 1792 Flaget sailed from Bordeaux, accompanied by fellow Sulpician John Baptist Mary David, and the then secular deacon Stephen Badin whose studies for the priesthood had been interrupted by the Revolution. They reached Philadelphia on March 26 and proceeded to Baltimore, arriving on March 29. After only two months in America, the Bishop of Baltimore, John Carroll, sent him to Fort Vincennes in the Indiana Territory to staff the Church of St. Francis Xavier, founded by Jesuit missionaries in 1748, before their Suppression and expulsion by British forces in 1763. There was a considerable number of French settlers and the mission which had gone without the presence of a resident priest for decades.