The film unfolds against the backdrop of the Jesuit Reductions, a remarkable initiative where Jesuit missionaries established autonomous missions to impart Christianity to indigenous populations. Central to the narrative is Father Gabriel, portrayed by Jeremy Irons, a Spanish Jesuit priest who journeys into the heart of the South American jungle with the aim of creating a mission for the local Guaraní Indians.
The narrative kicks off with a striking scene where a Jesuit missionary is bound to a cross by the Guaraní, who reside near the breathtaking Iguazu Falls. As the missionary is cast over the falls — still on the cross and praying fervently — his sacrifice ignites a flame of inspiration within Father Gabriel, compelling him to bravely scale the perilous falls in hopes of connecting with the tribe. Initially met with hostility and the prospect of death, Father Gabriel wins over the Guaraní after performing a poignant solo on his oboe, thus earning their trust over time.
Meanwhile, Rodrigo Mendoza, a mercenary and slave trader played by Robert De Niro, engages in the grim business of abducting natives to sell to local plantations, including one owned by the Spanish Governor Cabeza (played by Chuck Low). Mendoza's life takes a tragic turn when he discovers his fiancée, Cherie Lunghi, in a compromising position with his younger half-brother Felipe (portrayed by Aidan Quinn). In a fit of rage, he kills Felipe in a duel. Although he escapes legal consequences thanks to Cabeza, Mendoza succumbs to a deep depression. It is then that Father Gabriel steps in, urging him to seek redemption through appropriate penance. Mendoza decides to join the Jesuits on their journey back, lugging a heavy bundle that contains his armor and sword.
Upon reaching the outskirts of the Guaraní territory, Mendoza is initially met with wariness but is soon embraced by the natives, who remove his burdensome load in a touching scene. The mission, led by Father Gabriel, becomes a sanctuary for the Guaraní, filled with hope and education. Inspired by their acceptance, Mendoza finds a new purpose and receives a Bible from Father Gabriel, eventually taking vows to become a Jesuit himself under the guidance of Father Gabriel and his associate Father Fielding (played by Liam Neeson).
However, a looming threat arises as the Treaty of Madrid of 1750 shifts the control of the lands from the Spanish to the Portuguese, whose laws permit slavery. The Portuguese colonizers aim to enslave the indigenous people, and Cardinal Altamirano (portrayed by Ray McAnally), a Papal envoy and former Jesuit, is dispatched to assess the missions and determine their fate. Caught between the exploitation of the natives and the preservation of the Jesuit Order, Altamirano visits the mission, where he marvels at the thriving community and its accomplishments in both spirituality and economy.
At Father Gabriel's mission, he faces the daunting task of explaining to the Guaraní the impending closure of their sanctuary. When the Guaraní protest his authority, Father Gabriel and Mendoza, now under the threat of excommunication, vow to protect the mission from the encroaching plantation owners. They are divided in their methods: while Father Gabriel renounces violence as a sin against God, Mendoza takes a different path. He breaks his vows, instructing the natives in the art of European warfare and prepares to defend their home.
The narrative escalates when a joint force of Portuguese and Spanish soldiers launches an attack on the mission. With Mendoza, Fielding, and the Guaraní defending the sanctuary, they face overwhelming odds. Mendoza is fatally wounded during the confrontation, but the Guaraní's spirit is momentarily buoyed when they sing alongside Father Gabriel as the soldiers invade. However, the Portuguese commander orders a merciless attack during their sacred procession, resulting in devastating consequences as the priests and many Guaraní perish. In a final act of bravery, Fielding sacrifices himself to take down the Portuguese commander.
In the aftermath, the chilling dialogue between Cardinal Altamirano and Governor Don Hontar (played by Ronald Pickup) underscores the tragedy of their actions: Hontar states, "we must work in the world; the world is thus," to which Altamirano counters, "No, thus have we made the world. Thus have I made it."
In the poignant closing scene, a group of young children navigates the river back to the site of their community's massacre, salvaging remnants of their past while carrying a solemn memory forward. The film concludes with a powerful message, declaring that both Jesuits and others continue to advocate for the rights of indigenous peoples, encapsulated in the text of John 1:5: "The light shines in the darkness, and the darkness has not overcome it."
