In a dark room, Amerigo Bonasera, a Sicilian-born undertaker, describes his plight. Bonasera's daughter is disfigured as a result of a brutal attack by her boyfriend and his friends. He has come to the Godfather, Don Vito Corleone, to enact justice where the law has failed. While Don Corleone conducts business in his shadowy office at the Corleone Mall in Long Beach, Long Island, the wedding of his daughter, Constanzia "Connie" Corleone and Carlo Rizzo is underway in the courtyard. During the wedding scene, director Francis Ford Coppola introduces his audience to the vital members of the Corleone Crime Family. Sonny, Don Vito's eldest son, is the hot-headed, philandering Underboss of the Family. Sonny's younger brother, Fredo, is a simple-minded, ineffective party animal. Meanwhile, Michael, the youngest son, comes to the wedding dressed in his Marine uniform, accompanied by his WASP girlfriend, Kay Adams. Upon introducing her to his family and their "business", Michael assures Kay that he is not like his family.
The wedding guests are treated to an impromptu performance by Johnny Fontane, a famous crooner and actor - and Don Corleone's godson. Later, Johnny Fontane sits on Don Corleone's desk, lamenting the fact that he is desperate for a role in a new war film, but the studio head, Jack Woltz, has refused to consider him. After slapping his godson across the face for his display of weakness, Don Corleone promises to make Woltz "an offer he can't refuse". In Los Angeles, Tom Hagen tells Woltz that if he casts Johnny Fontane in the leading role, Hagen's anonymous client will help him with his union problems. Woltz explodes and insists that he will not be intimidated by "goombas", and sends Hagen away. Later, after finding out that Tom Hagen works for Don Corleone, Woltz has a change of heart, inviting the consigliere to his vast Hollywood estate. Woltz makes sure to show off Khartoum, his $600,000 stud horse. However, over dinner, Woltz tells Hagen that he cannot give Johnny Fontane the role because he seduced one of Woltz's proteges. Tom Hagen leaves calmly. The next morning, Woltz wakes up with the severed head of Khartoum tangled in his bedsheets.
Back in New York, Don Corleone, Sonny, Fredo, Tom Hagen, and caporegimes Tessio and Clemenza meet with Virgil "The Turk" Sollozzo, who requests a cash infusion and protection for his narcotics trade. Don Corleone refuses the offer - if he gets involved in the narcotics trade, he may lose valuable political connections. After the meeting, Don Corleone sends Luca Brasi to find out more about Sollozzo and the Tattaglia Family, who support his activities in New York. However, Sollozzo and Tattaglia are onto Don Corleone's move and kill Brasi. Later, Don Corleone is gunned down by Sollozo's thugs in the street. Meanwhile, Sollozzo has kidnapped Tom Hagen and tells him that the Don is dead. Sollozzo pushes Hagen to encourage Sonny to accept his deal. After his meeting with Tom Hagen, though, Sollozzo finds out that Don Corleone has survived the attack.
Michael finds out about the attack on his father by reading about it in the newspaper and immediately returns to the Corleone Mall. Sonny realizes that Paulie Gatto, the Don's bodyguard, sold him out and orders Gatto's execution. That same night, Sonny receives a package from Sollozzo, containing Luca Brasi's bulletproof vest wrapped around some dead fish, an old Sicilian message meaning "Luca Brasi sleeps with the fishes". The next day, Clemenza and Rocco Lampone take Paulie Gatto for a drive and murder him.
The following night, Michael goes to visit his father in the hospital, but finds out that Sollozzo has paid off the crooked Police Captain, McCluskey, to send away all the protection that Sonny had arranged. Afraid for his father's life, Michael jumps into action, hiding the Don in a different room and threatening McCluskey. In retaliation, McCluskey punches Michael, breaking his jaw. Back at the Corelone Mall, Tom Hagen warns Sonny that killing Sollozzo, and therefore, McCluskey, would ignite a war between the Corleones and the Tattaglias. Sonny backs down, but Michael is not convinced. He comes up with a plan to kill Sollozzo and McCluskey himself - if they don't, he asserts, the Don will be killed for sure.
The plan goes off without a hitch, and Michael murders Sollozzo and McCluskey. He then goes off to Sicily to hide, under the watchful eye of Don Tomassino. During his two years in Sicily, Michael falls in love with Apollonia, the daughter of a local cafe owner, and marries her. Meanwhile, Don Corleone comes back home to recover. Sonny - the acting Don - discovers that Carlo has been beating Connie, and retaliates by brutally beating his brother-in-law on the street. One day, Sonny gets a frantic call from a pregnant Connie after Carlo has abused her again and runs out of the house, determined to kill his brother-in-law. However, while stopped at a tollbooth, Sonny is ambushed by gunmen and killed. Don Corleone, now able to walk, insists that the Crime War must come to an end. He cries bitterly over Sonny's bullet-riddled corpse.
Back in Sicily, Don Tomassino tells Michael of his brother's untimely death and warns him that Corelone is no longer safe for him. As Michael prepares to move to another villa, his car explodes, accidentally killing Apollonia instead of Michael, the bomb's intended victim. In New York, at a meeting of the heads of the 5 Crime families, Don Corleone forges a truce. He promises not to enact vengeance for Sonny's death and they all come to an agreeable solution. However, at that meeting, Don Corleone realizes that Barzini, not Tattaglia, is responsible for Sonny's murder. Michael, who has since returned from Sicily, goes to New England to see Kay Adams. He proposes to her, and she accepts, on the condition that he will make good on his promise to make the Corleone Family business legitimate.
Michael takes over as the Don of the Corleone family, pushing Tom Hagen aside and relying on his father as consigliere. Tessio and Clemenza become increasingly frustrated at Michael's inaction while Barzini's people close in on the Corleones' business. Meanwhile, Michael is planning to move the family to Nevada to focus on their gambling interests. In Las Vegas, Michael meets with Moe Greene, the presiding Don, who refuses to sell his shares of his casino to the Corleone family. An aged Don Corleone meets with Michael at the Corleone Mall, and tells his youngest son that he always hoped he would become a politician - he never wanted him in the family business. Sadly, he tells Michael, whomever arranges a meeting with Barzini is the traitor within the family. One afternoon, while playing with Michael's son Anthony in the garden, Don Corleone collapses and dies. At the Don's funeral, Tessio tells Michael that Barzini wants to arrange a meeting. Michael and Tom Hagen know that this means Tessio has betrayed the family.
The day comes when Michael will be appointed godfather to Connie and Carlo's baby son. While Michael is in the church, his grand plan unfolds. The Corleone caporegimes carry out a violent massacre of all the heads of the New York Families, as well as Moe Greene in Las Vegas. After the baptism is over, Tom Hagen also has Tessio killed. Michael, who has discovered that Carlo aided the Barzini family in killing Sonny, has his brother-in-law strangled to death. Later, as Michael is preparing to move the Corleone family to Las Vegas, his hysterical sister Connie lashes out at him for killing Carlo. Kay asks Michael if Connie's accusations are true, and Michael lies to his wife, assuring her that he had nothing to do with Carlo's death. Relieved, Kay walks out of Michael's office to get a drink. When she looks back at her husband, his caporegimes are kissing his hand and calling him "Don Corleone".