In Buenos Aires, Argentina, Cardinal Jorge Mario Bergoglio (Jonathan Pryce) is informed that Pope John Paul II has passed away. The cardinals gather in Vatican City to elect a new Pope. The votes are split between Bergoglio, Joseph Ratzinger (Anthony Hopkins), and another cardinal, named Martini. Martini transfers his votes to Bergoglio, who doesn’t really want to be Pope, while Ratzinger campaigns hungrily for further votes, and becomes Pope Benedict. Bergoglio returns to Argentina with plans to do simple work and then retire. Ratzinger’s tenure as Pope is marked by controversy and claims he’s too conservative.
In 2012, an aide to the Pope leaks confidential documents, miring him in further scandal. Bergoglio travels back to the Vatican, and goes to see Ratzinger at his private summer residence. Bergoglio has asked for permission to retire, but Ratzinger feels that his resignation will look like a protest and criticism against him. Ratzinger grills Bergoglio on his more liberal views, and Bergoglio explains he can’t be a salesperson for a product he doesn’t believe in. He explains that while the church was dealing with its rituals and dogma, the real problems of inequality and injustice were ignored, especially the Church’s handling of sex abuses against children. Ratzinger angrily rebukes everything he says.
Ratzinger eats dinner alone, then meets with Bergoglio again, where he confesses he has had trouble hearing God as time passes. Bergoglio flashes back to 1956, where Young Jorge (Juan Minujin) considering being a priest and, unsure, asking for a sign, and hearing nothing. He got a job in science and a beautiful fiancee. On his way to see her, he walks by a church and walks in when he hears music. He goes to the confessional, and the priest explains that he felt god calling him to confessional, and no one came in until Jorge. He takes it as a sign, and breaks up with his fiancee and joins the church. Bergoglio tells Ratzinger he feels God telling him now to retire.
Bergoglio implores Ratzinger to play the piano for him, which he does. Ratzinger loosens up and watches some television with Bergoglio, and confesses to appreciating some company since he is always alone. The next day, Ratzinger is called back to Rome, so he and Bergoglio travel back by helicopter. Bergoglio brings up his retirement again, but Ratzinger ignores him. When his business is done, Ratzinger meets with Bergoglio again in a beautiful church. Ratzinger explains that he really brought Bergoglio to Rome not to accept his retirement, but instead because he is retiring. Bergoglio is shocked, saying Popes can’t resign, and tells him not to do it, saying it would damage the papacy. He explains that he knew he couldn’t retire if Bergoglio was resigning in case he was elected Pope. Bergoglio insists he couldn’t be Pope, doesn’t deserve to be Pope, and flashes back to 1976.
In 1976, when the Argentinian government was overthrown by military dictatorship. Many priests and nuns were murdered. In order to protect his priests, he compromises with the regime and ingratiates himself with them. He warns his old friend Esther, whose daughter is one of the many who has gone missing in the overthrow, that she is being watched, and she begs him to do something and not work with them. Jorge flees to his fellow priests and tells them to close the mission. They blame Jorge for not speaking out. He explains he was just trying to protect his order, and tells them to flee. They say fleeing the people goes against their faith, and that he is “drinking tea with killers”, and insist on staying, despite the fact that they will be without the church’s protection. They, along with Esther, are taken away and tortured by the military, and some, like Esther, are eventually killed. Jorge is able to hide some families in the seminary, but when the dictatorship falls he is cast out from his order and sent abroad.
Bergoglio stays outcast from 1984 to 1998, where he is still plagued with accusations of aiding in the tyranny. He preaches against income inequality and about helping the poor and continues to do good work. He is noticed and made Bishop, and lives a humble life, living small, doing what he perceives to be penance all through 2012. In present day, Bergoglio explains that he has failed in many ways and doesn’t deserve to be Pope, and Ratzinger tells him he is only human. and he needs to give himself the mercy he gives to others.
Flashbacks reveal that one of the priests who was tortured eventually escaped and reunited tearfully with Jorge and forgave him – though others did not. Ratzinger then asks Bergoglio to take his confession, and tells him how he shuffled a priest who was molesting boys around despite evidence. Bergoglio implores him to stay on as Pope and heal the wound, but Ratzinger tells him he cannot hear God anymore, only in the last few days and that he is telling him to leave. Bergoglio leaves the Vatican on friendly terms with Ratzinger.
In 2013, Ratzinger retires, shocking the world. Bergoglio is elected to be the newest pope. He addresses the crowd of gathered people, and thanks Ratzinger and asks the crowd to pray for him. He begins traveling the world, trying to better it and aid in helping the suffering of others. Later, in 2014, the two popes reunite to watch the World Cup together while eating pizza.