My Jesuit high school must have done a far better job of indoctrinating me than I thought at the time, because I found this film incredibly upsetting. Set in 18th Century South America, the story poses a set of moral challenges for its characters and thus its audience, for which Christian theology has clear answers, the Catholic church its own considerations, and human politics some additional complications.
Jeremy Irons is Father Gabriel, the film's Christ-like figure, a Jesuit missionary who has established rapport with a geographically isolated native tribe. He has taught them about God without shaming them; they remain naked and painted, but live in loving community. They have build a modest church, and he has taught them to sing and play musical instruments. The money generated by their labor goes back into the community.
Robert De Niro is Rodrigo Mendoza, an enemy at first to these natives, whom he captures and sells to the Portuguese as slaves. But after killing his brother in a duel over a woman, he is racked by guilt. He imprisons himself, and languishes for six months before Father Gabriel comes, and challenges him to seek forgiveness. Mendoza challenges the Father to accept his likely failure. The deal is done, and Gabriel brings Mendoza to the village atop the waterfall; a journey the haunted man makes carrying all of his metal armor and weaponry in a sack tied from ropes, wrapped around his chest. He carries his burden for days, climbing wet mountains, until one of Gabriel's fellow priests decides it is enough, and severs the cord. Relentless, Mendoza goes back down to where his penance has fallen, reties it to himself, and sets out again to climb the mountain. He is not free until they reach the village, and a native, recognizing the slave-trader turned penitent, cuts the cord. Mendoza becomes a priest, working alongside Gabriel to bring the village closer to God's kingdom on earth.
Political machinations, however, threaten their work. Spain (a Catholic country that does not allow slavery) proposes to cede this land to Portugal (a country that does allow slavery, whose colonies are in fact built upon it). A Cardinal is sent by the Catholic church to inspect the missions of the area, and though he is moved by the Jesuit's achievements, he nevertheless allows the Spanish government to pass the lands to the Portuguese (a political choice, the threat being that, if he doesn't, Portugal will expel the Jesuit order). From a moral point of view, this is the wrong choice: the preservation of an institution, even a religious institution, is of less consequence than the preservation of a population, particularly this sort of a population (cf. the Beatitudes: blessed are the poor, the meek, the pure of heart; those that hunger and thirst after righteousness).
The next moral decision is that of the missionaries and natives: when the Portugese soldiers come, will they peacefully stand their ground, or will they fight? The Catholic Church offers a Doctrine of Just War, with four requirements: 1) the damage inflicted by the aggressor on the nation or community of nations must be lasting, grave, and certain; 2) all other means of putting an end to it must have been shown to be impractical or ineffective; 3) there must be serious prospects of success; 4) the use of arms must not produce evils and disorders graver than the evil to be eliminated.
Mendoza takes up his arms. Father Gabriel chooses not to fight. Mendoza asks Gabriel for his blessing, but the Father will not give it. He says, "If might is right, than love has no place in the world." While he acknowledges that this might be the world in which they live, he sticks strongly to Christ's instruction to turn the other cheek, and refuses to take up arms. Mendoza, at least so far as the Just War Doctrine is concerned, would be justified in taking up arms, except that he has not point three on his side. The Portuguese soldiers slaughter the natives, who die with blood on their hands, having killed soldiers themselves to protect their home. And in the end, Gabriel, standing in front of the church with one hundred women and children, leads them singing to their slaughter.
What fills me with anger and confusion is the willingness of each Portuguese soldier to follow through with his "duty" and slaughter these innocents. Christ's way to reach these men would be to approach each individual, arms open in loving acceptance, offering forgiveness for the action he is about to take, and perhaps thus preventing it. That is to say, each soldier needed what Mendoza was given, not what Mendoza chooses to give. He has, thus, not completely learned Gabriel's lesson, and dies still ignorant, defiant as we by nature are.