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In 1979, as Michael Corleone is approaching 60, he regrets his ruthless rise to power and is especially guilt-ridden for having his brother, Fredo, murdered. He has semi-retired from the Mafia, leaving management of the Corleone family's New York business to enforcer Joey Zasa. Michael uses his tremendous wealth and power in an attempt to rehabilitate his reputation via numerous charitable acts. Michael and Kay have been divorced, and Kay was given custody of their children, Anthony and Mary.
At a ceremony in St. Patrick's Old Cathedral, Michael is named a Commander of the Order of St. Sebastian. At the following reception, Anthony tells his father that he is leaving law school to become an opera singer. Kay supports his decision, but Michael asks Anthony to complete his law degree. Anthony refuses to adhere to his father's wishes. Michael and Kay have an uneasy reunion, in which Kay reveals that she and Anthony know the truth about Fredo's death.
Vincent Mancini, Sonny Corleone's illegitimate son with Lucy Mancini, arrives at the reception. He is embroiled in a feud with Zasa, who has involved the Corleone family in major drug trafficking and turned Little Italy into a slum. Michael's sister, Connie, arranges a meeting between Vincent and Zasa. When Zasa calls Vincent a bastard, Vincent bites Zasa's ear. Vincent overpowers two hitmen sent to kill him and learns that Zasa was responsible. Michael, troubled by Vincent's fiery temper but impressed by his family loyalty, agrees to take him under his wing.
Knowing that Archbishop Gilday, head of the Vatican Bank, has accumulated a massive deficit, Michael offers the Bank $600 million in exchange for shares in International Immobiliare, an international real estate holding company known as "the world's biggest landlord", which would make him its largest single shareholder with six seats on the company's 13-member board of directors. He makes a tender offer to buy the Vatican's 25% share in the company, which will give him controlling interest. The Immobiliare's board quickly approve the offer, pending ratification in Rome by Pope Paul VI, who is gravely ill.
Don Altobello, an elderly New York Mafia boss and Connie's godfather, visits Michael, telling him that his old partners on the Commission want in on the Immobiliare deal. Michael wants the deal untainted by Mafia involvement and pays off the mob bosses from the sale of his Las Vegas holdings. Zasa receives nothing and, declaring Michael his enemy, storms out. Altobello follows Zasa, saying he will reason with him. Minutes later, a helicopter hovers outside the conference room and opens fire. Most of the bosses are killed, but Michael, Vincent, and Michael's bodyguard, Al Neri, escape.
Back in New York, Neri tells Michael that the surviving mob bosses made deals with Zasa. Believing Zasa lacks the mindset to mastermind the massacre, Michael is certain someone else was the mastermind. Michael forbids Vincent from killing Zasa, realizes that Altobello is the traitor, suffers a diabetic stroke, and is hospitalized. As Michael recuperates, Vincent and Mary begin a romantic relationship, while Neri and Connie give Vincent permission to retaliate against Zasa. During a street festival hosted by Zasa's Italian American civil rights group, Vincent kills Zasa. Michael berates Vincent for his actions and insists that Vincent end his relationship with Mary, explaining Vincent's involvement in the family's criminal enterprises endangers her life.
The family travels to Sicily for Anthony's operatic debut in Palermo at the Teatro Massimo. They stay with Don Tommasino, a long-time friend. Michael tells Vincent to convince Altobello of his desires to leave the Corleone family. Altobello introduces Vincent to Don Licio Lucchesi, a powerful Italian political figure and Immobiliare's chairman. Michael discovers that the Immobiliare deal is an elaborate swindle, conspired by Lucchesi, Archbishop Gilday, and Vatican accountant Frederick Keinszig. Michael visits Cardinal Lamberto, favored to become the next Pope, to discuss the deal. Lamberto persuades Michael to make his first confession in 30 years. Michael tearfully confesses that he ordered Fredo's murder, and Lamberto says Michael deserves to suffer but can be redeemed.
Altobello hires Mosca, a veteran hitman, to assassinate Michael. Mosca and his son, disguised as priests, kill Don Tommasino as he returns to his villa. While Michael and Kay tour Sicily, Michael asks for Kay's forgiveness, and they admit they still love each other. Michael receives word of Tommasino's death, and at the funeral vows never to sin again. After Pope Paul VI dies, Cardinal Lamberto is elected as Pope John Paul I, and the Immobiliare deal is to be ratified. The plotters against the ratification attempt to cover up their tracks. Vincent tells Michael that Altobello is plotting to have Mosca assassinate Michael. Michael sees that his nephew is a changed man and names him the new Don of the Corleone family, telling him he to adopt the Corleone name. In exchange, Vincent agrees to end his romance with Mary.
The family travels to Palermo to watch Anthony's performance in Pietro Mascagni's Cavalleria rusticana, a tale of murderous revenge in a Sicilian setting. Meanwhile, Vincent exacts his own revenge:

Keinszig is abducted by Vincent's men, who smother and then hang him from a bridge, making his death look like a suicide.
Don Altobello, also attending the opera, eats poisoned cannoli that Connie gives him. He dies as Connie watches from her opera box.
Al Neri travels to the Vatican, where he shoots Archbishop Gilday.
Finally, CalÃ² (Tommasino's former bodyguard, assigned to protect Michael while he was in Sicily during the events of the first film) meets with Don Lucchesi at his office, claiming to bear a message from Michael. As he whispers the message, "Power wears out those who don't have it", to Lucchesi, CalÃ² stabs him in the neck with his own spectacles.
Just hours after he approves the Immobiliare deal, the Pope is served poisoned tea by Archbishop Gilday and dies soon afterward. Mosca, still disguised as a priest and armed with a sniper rifle, descends upon the opera house during Anthony's performance and eliminates three of Vincent's men, but is unable to shoot Michael. The assassin retreats and attempts to kill Michael outside the opera house. Mosca fires twice but unintentionally kills Mary. Vincent shoots him dead.
Michael remembers all the women he has lost as a montage of Mary, Kay, and Apollonia is shown. An elderly Michael sits alone in the garden of Don Tommasino's Sicilian villa and suddenly slumps over in his chair, falling to the ground.
With whom does Vincent being a romantic relationship while Michael recuperates in the hospital?
Mary