- In 1901, the family of nine-year-old Vito Andolini is killed in Corleone, Sicily, after his father insults local Mafia chieftain Don Ciccio. Vito escapes to New York City and is registered as "Vito Corleone" on Ellis Island.
In 1958, during his son's First Communion party at Lake Tahoe, Michael Corleone has a series of meetings in his role as the Don of his crime family. Corleone caporegime Frank Pentangeli is dismayed that Michael refuses to help defend his Brooklyn territory against the Rosato brothers, who work for Michael's business partner Hyman Roth. That night, Michael leaves Nevada after surviving an assassination attempt at his home.
- In 1917, Vito Corleone lives in New York with his wife Carmela and son Sonny. He loses his job due to Don Fanucci insisting that his nephew work there; Peter Clemenza invites Vito to unwittingly take part in a burglary.
Michael suspects Roth planned the assassination, but meets him in Miami and feigns ignorance. In New York, Pentangeli attempts to maintain Michael's façade by making peace with the Rosato family but they attempt to kill him. Roth, Michael, and several of their partners travel to Havana to discuss their future Cuban business prospects under the cooperative government of Fulgencio Batista; Michael becomes reluctant after reconsidering the viability of the ongoing Cuban Revolution. On New Year's Eve, he attempts to have Roth and Roth's right-hand man, Johnny Ola, killed, but Roth survives when Michael's bodyguard is discovered and shot by police. Michael discovers that his brother, Fredo, betrayed him after Fredo inadvertently reveals that he knows Ola after claiming they had never met. Batista abruptly abdicates due to rebel advances; during the ensuing chaos, Michael, Fredo, and Roth separately escape to the United States. Back home, Michael learns that his wife Kay has miscarried.
- By 1920, Vito and Carmela have had two more sons, Fredo and Michael. Vito's criminal conduct attracts the attention of Fanucci, who extorts him. His partners, Clemenza and Salvatore Tessio, wish to avoid trouble by paying in full, but Vito insists that he can convince Fanucci to accept a smaller payment by making him "an offer he won't refuse". During a neighborhood festa, he stalks Fanucci to his apartment and shoots him dead.
In Washington, D.C., a Senate committee on organized crime is investigating the Corleone family. Having survived the earlier attempt on his life, Pentangeli agrees to testify against Michael, who he believes had double-crossed him, and is placed under witness protection.
- Now a respected figure in his community, Vito is approached for help by a widow who is being evicted. After an unsuccessful negotiation with Vito, the widow's landlord asks around, learns of Vito's reputation, and hastily agrees to let the widow stay on terms very favorable to her. In the meantime, Vito and his partners are becoming more and more successful, with the establishment of their business, "Genco Pura Olive Oil Company".
On returning to Nevada, Fredo privately explains himself to Michael; feeling resentful at being disregarded, he had helped Roth in expectation of something in return—unaware, he claims, of the plot on Michael's life. He also informs Michael that the Senate lawyer, Questadt, is working under Roth's payroll. Michael responds by disowning Fredo, and tells his capo that nothing is to happen to Fredo while their mother is alive. Michael is unable to reach the heavily-guarded Pentangeli, so sends for Pentangeli's brother from Sicily, resulting in Pentangeli renouncing his previous statement; the hearing dissolves in uproar.
Kay reveals to Michael that she actually had an abortion, not a miscarriage, and that she intends to remove their children from Michael's criminal life. Outraged, Michael strikes Kay, banishes her from the family, and takes custody of the children.
- In 1923, Vito, along with his family, visits Sicily for the first time since emigrating. He and business partner Tommasino are admitted to Don Ciccio's compound, ostensibly to ask for Ciccio's blessing on their olive oil business. Vito exacts his childhood vengeance by killing Ciccio after revealing his former identity, but as they escape, Tommasino is shot in the leg and suffers a permanent disability.
Carmela Corleone dies. At the funeral, Michael appears to forgive Fredo.
Roth is refused asylum and denied entry to Israel. He is forced to return to the United States. Over the dissent of consigliere Tom Hagen, Michael sends caporegime Rocco Lampone to intercept and shoot Roth on arrival. Rocco is shot dead by federal agents after completing his mission. At the witness protection compound, Hagen reminds Pentangeli that failed plotters against the Roman Emperor often committed suicide and assures him that his family will be cared for. Pentangeli later slits his wrists in his bathtub. Al Neri, acting on Michael's orders, assassinates Fredo out on the lake.
- On December 7, 1941, the Corleone family gathers in their dining room to surprise Vito for his birthday. Michael announces that, in response to the attack on Pearl Harbor, he has left college and enlisted in the United States Marine Corps, leaving Sonny furious, Tom incredulous, and Fredo the only brother supportive. Vito is heard at the door and all but Michael leave the room to greet him.
Michael sits alone by the lake at the family compound.