Back in Sicily in 1901, a young Vito Andolini attends his father’s funeral with his mother. During the funeral, his brother is also killed by the local mafia leader, Don Ciccio. Vito’s mother pleads for Ciccio to spare him, but Ciccio refuses, claiming Vito will only return as a man to exact revenge. Ciccio’s men kill Vito’s mother, and Vito escapes to New York, where he’s given the name Vito Corleone.
In 1958, Michael Corleone throws a lavish party at his family compound in Tahoe for his son’s first communion. At the party, a Senator from Nevada tries to shake the family down for bribe money to get a license for a new casino. Michael refuses the Senator’s offer. Frank, a family member, comes to Michael to request support in a war with the Rosato brother back in New York. Michael refuses, however, since the Rosato brother are backed by the wealthy Jewish mobster from Miami, Hyman Roth. After the party, an assassination attempt against Michael fails. Michael puts Tom Hagen in charge and goes off to meet Roth.
Back in New York in 1917, Vito Corleone scrapes by making an honest living for his family. He loses his job, however, when Don Fanucci, a local mob boss, orders Vito’s employer to give his job to the Don’s nephew. Meanwhile, Vito’s neighbor asks that he stash some guns for him, and as repayment allows him to accompany him on a burglary job.
In 1958, Michael meets with Roth and tell him that Frank was behind the assassination attempt. But Michael then travels to New York where he tells Frank it was actually Roth. Michael asks Frank to make a deal with the Rosato brother so that Roth will not suspect Michael, and Michael can exact his revenge against Roth. Frank makes a deal with the Rosato brother, but he’s double crossed, and when the Rosato brother try and fail to assassinate him, they him, “Michael Corleone says hello” and wrap a piano wire around his neck.
Meanwhile, Michael meets with Roth and other business owners to bribe the Cuban president in order to grease the wheels on some business dealings in Cuba. Michael gets cold feet about handing over $2 million and cash, and Roth gets testy with Michael. When they are out on the town, Michael realizes that Fredo is the insider in the family that betrayed him and made the assassination attempt possible. Michael tells Fredo he knows, and Fredo flees as Cuban revolutionaries take over the capital, and the president abdicates. Michael orders a hit on Roth, which is unsuccessful. But Michael manages to escape Cuba.
Then we travel back in time to a young Vito Corleone, who now has three children. Don Fanucci tries to extort Vito and his partners. But Vito won’t lie down. Vito lies in wait and murders Don Fanucci in his threshold. This catapults Vito into local stardom, and becomes The Godfather.
Michael, however, is facing problems of his own. He is facing a Senate investigation into the family. The investigation goes nowhere until Frank agrees to testify against him. However, when Frank comes to testify, his brother is present from Sicily. Frank changes his mind and lies to the Senate committee. After Michael beats the Senate investigation, Kaye tries to leave him. Michael won’t let her leave, and Kaye reveals that her recent miscarriage was actually an abortion.
Then we follow a young Vito Corleone who returns to Sicily and is celebrated. He pays Don Ciccio a visit and cuts his belly open as revenge for killing his family.
Meanwhile, Michael’s mother dies, and Michael orders a hit on Fredo, who was allowed to reenter the family compound. Fredo is shot in the back, and Tom visits Frank in FBI custody and suggests that he kill himself. Frank takes the suggestions, with an implied promise that Michael will care for Frank’s family. Roth is shot on his return to Miami by one of Michael’s men.
In a final flashback, Michael celebrates his father’s fiftieth birthday with his family. Michael sits with his siblings and Tom while they lament about the Japanese attack on Pearl Harbor. Sonny opines that it’s foolish and unthinkable that people would sign up to die for something as nebulous as their country and that only family is worth dying for. Michael disagrees and tells them that he had just enlisted into the Marines out of a sense of patriotism. Sonny is disgusted and leaves angrily. The others follow Sonny, and Michael is left alone as the other greet their father for his birthday.
The film concludes on one final shot of Michael in the present day, all alone in the darkness in his Tahoe boathouse.