In colonial South America, a Jesuit priest (Jeremy Irons) attempts to start a mission to convert a tribe of natives living above the falls, after a subordinate of his was killed trying to do the same. Later, he takes on the role of confessor to an ex-slaver (Robert DeNiro), wallowing in despair after committing a grave sin. Assisting the priest, the slaver toils to find repentance and forgiveness.
Meanwhile, the European powers have decided to redraw the map of the New World. The proposed alteration would transfer ownership of these lands from Spain to Portugal. A papal legate (Ray McAnally) has been sent to allegedly determine the current state of the missions here and judge whether this decision would be right for the Church. The key point is that the change would make enslaving the natives legal. The story unfolds as the two protagonists respond to the transfer of power in very different ways.
