Jesuit priest Father Gabriel (Irons) goes to South America for missionary work, hoping to convert some natives to Christianity. He builds a mission (hence the name of the movie), and is joined by Rodrigo Mendoza (De Niro), a former slave trader seeking redemption.
When the Spanish government sells the territory to Portugal, the Portuguese government wants to capture the natives for slave labor. Mendoza and Gabriel oppose this and resolve to defend the mission, though disagree on how to accomplish the task.
This film provides examples of the following:
- Actual Pacifist: Father Gabriel refuses to fight back physically against the Portuguese, unlike Mendoza.
- All for Nothing: In less than 20 years, Jesuits have been suppressed, making the sacrifice of the handful of missions in the Paraguay meaningless. In the book, Altamirano is tormented by this to the end of his days.
- All There in the Manual: The script only adapts the second half of the novel, thus numerous things are completely lost in the film. Most notably, the entire backstory of Mendoza is ommited, leaving only the fated duel with his own brother and thus stripping the movie out of the entire emotional impact of that moment.
- The Atoner: Mendoza. He killed his younger brother in a fit of jealousy for sleeping and getting infatuated with his bride, and gets depressed. As a form of penitence, Mendoza packs a bag of armor and weapons, symbolizing his guilt, and climbs to get to father Gabriel's mission, who proposed him to do so. When he finally arrives, a Guaraní man frees him from the load and Mendoza starts to shed tears, finally having his pardon over his crime.
- The Bad Guy Wins: Hontar and Cabeza conquer the Guaraní territories for the Crowns of Spain and Portugal at a very high cost, much to Altamirano's horror.
- Big Bad Duumvirate: Cabeza, the hot blooded and bald Spaniard, and Hontar, the cold and calculating Portuguese, who represent to interests of their crown countries in the Guaraní territories.
- Book-Ends: The film starts with Altamirano staring at the audience as he is writing the letter for His Holiness and the post-credits scene has him staring again at the audience as soon as he finishes his letter.
- Doomed Moral Victor: The Jesuits and the Guarani, in the end.
- Downer Ending: Gabriel, Mendoza, Fielding, and most of the Guaraní are killed by the Portuguese strike force. However, the ending quote suggests all is not lost."The light shines in the darkness, and the darkness has not overcome it." - John 1:5
- Flynning: Averted in the duel between Rodrigo and his brother, which lasts only a few seconds, and portrays real techniques in rapier fencing (though they use smallswords) like using a knife (usually it was a dagger) in the left hand.
- Foregone Conclusion: Cardinal Altamirano makes the decision he does in order to prevent the suppression of the Society of Jesus. Historically, the Jesuits were suppressed anyway just a few years later.
- Good Shepherd: Father Gabriel is about as saintly as they come.
- HeelFace Turn: Rodrigo Mendoza is a slaver who undergoes penance and eventually dies protecting those he had hurt in the past.
- I Did What I Had to Do: Cabeza and Hontar, the Spanish and Portuguese governors, try to justify their actions this way. Cardinal Altamirano (who is clearly guilt ridden after condemning the missionaries) doesn't buy it.
- Inevitable Waterfall: The most famous shot from the movie is of a priest being tied to a cross and being sent downriver to Iguazu Falls. It's been also used as an ad poster.
- Irish Priest: Father Gabriel is a missionary from Ireland.
- Ordered Apology: Rodrigo is ordered to deliver an apology to Governor Cabeza by his Jesuit brothers after publicly calling him out on his lies. He does so, but it's executed with such over-the-top humility that it's clear Rodrigo is just taking the piss. Cabeza grudgingly accepts the "apology".
- Pragmatic Adaptation: The movie skips first half of the book, containing backstory for both Rodrigo and Gabriel. This unfortunately removes most of the emotional impact from the original story, especially the implication why someone like Mendoza broke down after killing his brother. But should that part be kept, the movie would take at least another 60 minutes more, bloating it into 3 hours, if not longer.
- Real Men Love Jesus: Most of the main characters are either priests or convert at some point and often their faith lead to moments of badassery such as Mendoza climbing up a mountain with a coffin full of armor and weapons tied to him.
- Redemption Equals Death: Mendoza's ultimate fate.
- Redemption Quest
- Retired Monster: Rodrigo Mendoza was one of the most prominent and ruthless slave catchers in the area, well-known for his brutality and lack of compassion to just about anyone. He eventually sides with and defends the very people he was tormenting and enslaving. It is especially prominent in the original novel, where his backstory takes roughtly half of the text, in detail covering his more and more inhuman actions.
- Scenery Porn: The winner of the Academy Award for Best Cinematography in 1987, no less! Iguazu Falls, the mission of San Miguel... All beautifully shot in its magnificency and colors. As told by Altamirano in his narration, he was so truly astonished by its beauty and sad that he compared the destruction of the mission of San Miguel with a surgeon cutting off an important limb.
- Seldom-Seen Species: The choir boy has a pet marmoset in a time when the usual South American monkey was either a capuchin monkey or a squirrel monkey. The Guaraní are seen hunting a collared peccary, which could easily be mistaken as a wild hog or pig for common viewers, and offer it to Mendoza to kill it, but he refuses. Also, Hontar's first scene has him embracing his exotic pet, a three-toed sloth, who weren't as popular as in the Internet days, describing it as a fascinating creature.
- Soundtrack Dissonance: A triumphant choral piece (called "Vita Nostra" in the soundtrack) plays when the Guarani are building their church - and when they attack the Portuguese at the end despite certain to lose. Or perhaps not dissonant since they're Doomed Moral Victors.
- Tin Man: Rodrigo, especially in the novel. He spend most of his youth and adulthood doing progressively worse and worse deeds, eventually repressing his emotions and guilt to the point where everyone is convinced such monster simply can't have feelings. Then he finds the only woman capable of understanding and defrosting him... and we all know how it ended.
- To Be Lawful or Good: The Cardinal has a choice between pulling support for the Guaraní, dooming them, or letting the Catholic Church be condemned. He chooses the former. Also counts as a Sadistic Choice; whatever the Cardinal decides, one group is going to end up being persecuted; the natives, or the Jesuits.
- My God, What Have I Done?: Cardinal Altamirano at the end.Hontar: We must work in the world, your eminence. The world is thus.
Altamirano: No, Señor Hontar. Thus have we made the world... thus have I made it.
- Who Dares?: Don Cabeza doesn't take kindly to Mendoza calling him out on his lies:Cabeza: I cannot and will not accept a challenge from a priest! His cloth protects him!
Mendoza: My cloth protects you!