In The Godfather Part III, set in 1979-80, Michael, now in his 60s, has moved back to New York and taken great steps to make the family legitimate. He has turned over control of his New York criminal interests to longtime enforcer Joey Zasa, sold his gambling interests to the other Mafia families and reorganized his vast business holdings as the "Corleone Group". Wracked with guilt over his ruthless rise to power, he is using his wealth to restore his reputation through numerous acts of charity. The Vatican has named him a Commander of the Order of Saint Sebastian for his good works. That same day, he has an uneasy reunion with Kay, who tells him that she doesn't want Anthony to have anything to do with the Corleone "legacy", and that both she and Anthony know the truth about Fredo's death.
Michael's new connection to the Church gives him the opportunity to purchase a controlling stake in the large property company, Immobiliare. He also takes Sonny's illegitimate son Vincent Mancini as his protégé. The relationship is not without friction, however. Michael is deeply troubled by Vincent's impulsiveness and fiery temper, but even more so by his romance with Michael's daughter Mary; he fears that Vincent's growing involvement in the "family business" will put her in danger.
On the night Michael announces that he is dissolving his gambling empire, Zasa wipes out most of The Commission in an elaborate helicopter attack in Atlantic City; Michael escapes with Vincent's help. Michael quickly realizes that his longtime friend, Don Altobello, was actually in on the conspiracy to kill him. Traumatized by the attack, Michael has a diabetic stroke, leaving him briefly incapacitated. (Coppola reveals in his audio commentary that Michael was seen drinking a lot of water in the first two films—subtle hints that he was a diabetic.) In his absence, Connie gives Vincent and Neri the go-ahead to kill Zasa.
Michael later returns to Sicily to watch Anthony make his operatic debut at the Teatro Massimo. Suspecting that Altobello might try to make another attempt on his life, he has Vincent go to Altobello and pretend to defect. He takes Kay on a tour of Sicily, during which he asks her forgiveness. Each admits to the other that they still love each other and always will.
At the same time, the Immobiliare deal stalls, supposedly because Pope Paul VI himself must sign off on it. Michael eventually learns that the Immobiliare deal is actually an elaborate swindle concocted by Immobiliare chairman Licio Lucchesi, who has schemed with Vatican Bank head Archbishop Gilday and accountant Frederick Keinszig to steal a fortune from the Vatican Bank and use Michael's "investment" to cover their tracks. Hoping to salvage the deal, Michael seeks the assistance of Don Tommasino, who directs him to Cardinal Lamberto (the future Pope John Paul I), to whom Michael makes his first confession in 30 years, breaking down in tears while admitting that he ordered Fredo's murder. Lamberto tells Michael that it is just that he suffers for his terrible sins, but that he still has a chance for redemption.
Michael soon becomes aware of an assassin, Mosca, whom Altobello, in league with the plotters, had hired to kill him. Mosca kills Tommasino, and Michael vows before his old friend's coffin to sin no more.
Vincent reports that Lucchesi is behind the attempts on Michael's life, working hand in glove with Altobello. Vincent insists on striking back. Weary of the bloody, lonely life of a Don, Michael retires and makes his nephew the new head of the family, on condition that he end the relationship with Mary. That night, Michael, reconciled with Kay and Anthony, watches his son perform in the opera Cavalleria Rusticana. At the same time, Vincent, with Michael's tacit blessing, wipes out Lucchesi, Gilday and Keinszig in a bloody wave of murders. That same night, however, Mosca inadvertently kills Mary in an assassination attempt on her father. Mary's death breaks Michael's spirit, and he cries out in agony over her corpse. He retires to Sicily, where he dies years later, completely alone. (According to a timeline graphic included in a The Godfather DVD box set, Michael Corleone's death occurs in 1997.)
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