On the occasion of his only daughter Connie's wedding, Vito Corleone hears requests in his role as the Godfather, the Don of a New York crime family. Vito's youngest son, Michael, wearing a Marine Corps uniform, introduces his girlfriend, Kay Adams, to his family at the reception. Johnny Fontane, a famous singer and godson to Vito, seeks his help in securing a movie role; Vito dispatches his consigliere, Tom Hagen, to Los Angeles to influence the abrasive studio head, Jack Woltz into giving Johnny the part. Woltz is unmoved until he wakes up in bed with the severed head of his prized stallion.

Shortly before Christmas 1945, drug baron Virgil "The Turk" Sollozzo, backed by the Tattaglia crime family, asks Don Corleone for both investment in his narcotics business and protection through his political connections. Vito declines, wary of involvement in a dangerous new trade that risks alienating political insiders. Suspicious, he sends his enforcer, Luca Brasi, to spy on them. Solozzo has his men gun down Vito in the street, then kidnaps Hagen. With Vito's first-born Sonny Corleone in command, Hagen is pressured to persuade Sonny to accept Sollozzo's deal, then released. Vito survives the attack, but at the hospital Michael thwarts a second attempt on his father's life; Michael's jaw is broken by NYPD Captain Marc McCluskey, who is also Sollozzo's bodyguard. Sonny retaliates for the attacks on his father by having Tattaglia's son killed. The family receives two fish wrapped in Brasi's bullet-proof vest, indicating that Luca "sleeps with the fishes." Michael plots to murder Sollozzo and McCluskey: on the pretext of settling the dispute, Michael agrees to meet them in a Bronx restaurant and, retrieving a planted handgun, kills both men.

Despite a clampdown by the authorities, the Five Families erupt in open warfare and Vito's sons fear for their safety. Michael takes refuge in Sicily, and his brother,Fredo, is sheltered by the Corleone's Las Vegas casino partner, Moe Greene. Sonny attacks his brother-in-law Carlo on the street for abusing his sister and threatens to kill him if it happens again. When it does, Sonny speeds for their home but is ambushed at a highway toll booth and riddled with sub-machine gun fire. While in Sicily, Michael meets and marries Apollonia Vitelli, but their euphoria is shattered when a car bomb intended for him takes her life.

Devastated by Sonny's death, Vito moves to end the feuds. Realizing that the Tattaglias are controlled by the now-dominant Don Emilio Barzini, Vito assures the Five Families that he will withdraw his opposition to their heroin business and forgo avenging his son's murder. His safety guaranteed, Michael returns home and enters the family business. He and Kay reunite and marry the next year.

With his father semi-retired, and his brother too weak, Michael now heads the family, promising Kay the business will be legitimate within five years. To that end, he insists Hagen relocate to Las Vegas and relinquish his role to Vito because Tom is not a "wartime consigliere"; the older man agrees Tom should "have no part in what will happen" in the coming battles with rival families. When Michael travels to Las Vegas to buy out Greene's stake in the family's casinos, their partner derides the Corleones for being run out of New York; Michael is dismayed to see that Fredo has fallen under Greene's sway.

Vito suffers a fatal heart attack. At his funeral, Tessio, a Corleone capo, asks Michael to meet with Don Barzini, signalling Tessio's betrayal as Vito had forewarned that someone close to Michael would do. The meeting is set for the same day as the christening of Connie’s baby. While Michael stands at the altar as the child's godfather, Corleone assassins murder the other New York dons and Moe Greene. Tessio is executed for his treachery; Michael extracts Carlo’s confession to his involvement in setting up Sonny's murder for Barzini, and Clemenza garrotes Carlo with a wire. Kay tries to comfort Connie when she accuses Michael of murdering her husband and ordering the other executions and is relieved when he finally denies it. However, when the capos arrive, they address her husband as Don Corleone.