Plot

At the wedding reception of Don Vito Corleone's daughter Connie and Carlo Rizzi in the late summer of 1945, Vito, the head of the Corleone Mafia family – who is known to his friends and associates as Godfather – and Tom Hagen, the Corleone family lawyer and consigliere (counselor), are hearing requests for favors from friends and associates, because "no Sicilian can refuse a request on his daughter's wedding day". Meanwhile, the Don's youngest son Michael, who has returned from World War II service as a decorated war hero, tells his girlfriend Kay Adams anecdotes about his father's criminal life, reassuring her that he is not like his family.

Among the guests at the celebration is the famous singer Johnny Fontane, Corleone's godson, who has come from Hollywood to petition for help in landing a movie role that will revitalize his flagging career. Jack Woltz, the head of the studio, will not give Fontane the part, but Don Corleone explains to Johnny: "I'll make him an offer he can't refuse." Hagen is dispatched to California to fix the problem, but Woltz angrily tells him that he will never cast Fontane in the role, for which he is perfect, because Fontane seduced and "ruined" a starlet that Woltz favored. The next morning, Woltz wakes up to find the bloody severed head of his prize stud horse in the bed with him. Woltz gives in.

Upon Hagen's return, the family meets with Virgil "The Turk" Sollozzo, who is being backed by the rival Tattaglia family. He asks Don Corleone for financing and political and legal protection for the importation and distribution of heroin, but despite the huge amount of money to be made, Corleone refuses, explaining that his political influence would be jeopardized by a move into the narcotics trade. The Don's oldest son, hotheaded Sonny, who had earlier expressed to the Don his support of the family entering into the narcotics trade, breaks rank during the meeting and questions Sollozzo's assurances as to the Corleone Family's investment being guaranteed by the Tattaglia Family. His father, angry at Sonny's dissension in front of a non-family member, privately rebukes him later. Don Corleone then dispatches his top button man (hit man), Luca Brasi, to infiltrate Sollozzo's organization and report back with information.
Soon after his refusal to support Sollozzo, Don Corleone is shot several times in an assassination attempt, and it is not immediately known whether he has survived. Meanwhile, Sollozzo and the Tattaglias kill Luca Brasi. Sollozzo then abducts Tom Hagen and persuades him to offer Sonny the deal previously offered to his father. Enraged, Sonny refuses to consider the deal, and issues an ultimatum to the Tattaglias – turn over Sollozzo or face war. They refuse, and Sonny responds by having Bruno Tattaglia, son of Don Phillip Tattaglia, killed.

Michael, who is considered a "civilian" by the other Mafia families, not involved in mob business, visits his father in the hospital, but is shocked to find there is no one guarding him. Realizing that his father is again being set up to be killed, he calls Sonny with a report, moves his father to another room, and goes outside to watch the door. With the help of Enzo the baker, who feels indebted to the Don and has come by the hospital to pay his respects, he bluffs away Sollozzo's men. Police cars soon appear with the corrupt Captain McCluskey, who breaks Michael's jaw when he insinuates that McCluskey is being paid by Sollozzo to set up his father. Just then, Hagen arrives with "private detectives" licensed to carry guns to protect Don Corleone, and takes Michael home.

Following the attempt on the Don's life at the hospital, Sollozzo requests a meeting with the Corleones, which Captain McCluskey will attend as Sollozzo's bodyguard, and Michael volunteers to kill both men during the meeting. This initially amuses Sonny and the other senior members of the family, however, Michael convinces them that he is serious, and that killing Sollozzo and McCluskey is in the family's interest: "It's not personal. It's strictly business." Although cops are usually off limits for hits, Michael argues that since McCluskey is serving as Sollozzo's bodyguard he is fair game.

At the meeting, after being searched by McCluskey, Michael excuses himself to go to the restroom, where he retrieves a planted revolver and immediately assassinates Sollozzo and McCluskey. For his safety Michael is sent to Sicily, while the Corleone family prepares for all-out warfare with the rest of the Five Families, united against the Corleones, as well as a general clampdown on the mob by the police and government authorities. In Sicily, Michael lives under the protection of Don Tommasino, an old friend of the family. While there, he falls in love with and marries a local girl, Apollonia Vitelli, who is later killed by a car bomb intended to assassinate Michael.

Back in New York, Don Corleone returns home from the hospital and is distraught to learn that it was Michael who killed Sollozzo and McCluskey. Some months later, in 1948, Sonny severely beats Carlo Rizzi for brutalizing the pregnant Connie, and threatens to kill him the next time he abuses her. An angry Carlo responds by plotting with Tattaglia and Don Emilio Barzini, the Corleones' chief rivals, to have Sonny killed. Carlo beats Connie again in order to lure Sonny out. Furious, Sonny drives off alone to fulfill his threat. On the way, he is ambushed and machine-gunned to death in his car.
Soon after his refusal to support Sollozzo, Don Corleone is shot several times in an assassination attempt, and it is not immediately known whether he has survived. Meanwhile, Sollozzo and the Tattaglias kill Luca Brasi. Sollozzo then abducts Tom Hagen and persuades him to offer Sonny the deal previously offered to his father. Enraged, Sonny refuses to consider the deal, and issues an ultimatum to the Tattaglias – turn over Sollozzo or face war. They refuse, and Sonny responds by having Bruno Tattaglia, son of Don Phillip Tattaglia, killed.

Michael, who is considered a "civilian" by the other Mafia families, not involved in mob business, visits his father in the hospital, but is shocked to find there is no one guarding him. Realizing that his father is again being set up to be killed, he calls Sonny with a report, moves his father to another room, and goes outside to watch the door. With the help of Enzo the baker, who feels indebted to the Don and has come by the hospital to pay his respects, he bluffs away Sollozzo's men. Police cars soon appear with the corrupt Captain McCluskey, who breaks Michael's jaw when he insinuates that McCluskey is being paid by Sollozzo to set up his father. Just then, Hagen arrives with "private detectives" licensed to carry guns to protect Don Corleone, and takes Michael home.

Following the attempt on the Don's life at the hospital, Sollozzo requests a meeting with the Corleones, which Captain McCluskey will attend as Sollozzo's bodyguard, and Michael volunteers to kill both men during the meeting. This initially amuses Sonny and the other senior members of the family, however, Michael convinces them that he is serious, and that killing Sollozzo and McCluskey is in the family's interest: "It's not personal. It's strictly business." Although cops are usually off limits for hits, Michael argues that since McCluskey is serving as Sollozzo's bodyguard he is fair game.

At the meeting, after being searched by McCluskey, Michael excuses himself to go to the restroom, where he retrieves a planted revolver and immediately assassinates Sollozzo and McCluskey. For his safety Michael is sent to Sicily, while the Corleone family prepares for all-out warfare with the rest of the Five Families, united against the Corleones, as well as a general clampdown on the mob by the police and government authorities. In Sicily, Michael lives under the protection of Don Tommasino, an old friend of the family. While there, he falls in love with and marries a local girl, Apollonia Vitelli, who is later killed by a car bomb intended to assassinate Michael.

Back in New York, Don Corleone returns home from the hospital and is distraught to learn that it was Michael who killed Sollozzo and McCluskey. Some months later, in 1948, Sonny severely beats Carlo Rizzi for brutalizing the pregnant Connie, and threatens to kill him the next time he abuses her. An angry Carlo responds by plotting with Tattaglia and Don Emilio Barzini, the Corleones' chief rivals, to have Sonny killed. Carlo beats Connie again in order to lure Sonny out. Furious, Sonny drives off alone to fulfill his threat. On the way, he is ambushed and machine-gunned to death in his car.
Instead of seeking revenge for Sonny's killing, Don Corleone meets with the heads of the Five Families to arrange an end to the war. Not only is it draining all of their assets and threatening their survival, but ending the conflict is the only way that Michael can return home safely. Reversing his previous decision, Vito agrees that the Corleone family will provide political protection for Tattaglia's traffic in heroin. At the meeting, Don Corleone determines that Don Barzini, not Tattaglia, was ultimately behind for the mob war and Sonny's death.

With his safety guaranteed, Michael returns from Sicily. More than a year later, he reunites with his former girlfriend, Kay, telling her that he wants to marry her. With the Don semi-retired, Sonny dead and middle brother Fredo considered incapable of running the family business, Michael is now in charge, and promises Kay to make the family completely legitimate within five years.

Peter Clemenza and Salvatore Tessio, two Corleone Family caporegimes (captains) complain that they are being pushed around by the Barzini Family and ask permission to strike back, but Michael refuses. He plans to move the family operations to Nevada and after that, Clemenza and Tessio may break away to go on their own. Michael further promises that Connie's husband, Carlo, is going to be his right hand man in Nevada. Tom Hagen has been removed as consigliere and is now merely the family's lawyer, with Vito serving as consigliere. Privately, Hagen complains about his change in status, and also questions Michael about a new regime of "soldiers" secretly being built under Rocco Lampone. Don Vito explains to Hagen that Michael is acting on his advice.

In Las Vegas Michael is greeted by Fredo and Johnny Fontane in the hotel-casino partly financed by the Corleones, and run by Moe Greene. Michael explains to Johnny that the Family needs his help in persuading his friends in show business to sign long-term contracts to appear at the casino. In a meeting with Moe Greene, Michael offers to buy out Greene but is rudely rebuffed. Greene believes the Corleones are weak and that he can secure a better deal from Barzini.

Michael returns home. In a private meeting, Vito explains his expectation that the Family's enemies will attempt to kill Michael by using a trusted associate to arrange a meeting as a pretext for assassination. Shortly afterwards, Vito dies of a heart attack while playing with his young grandson Anthony in his tomato garden. During the funeral, Tessio conveys a proposal for a meeting with Barzini, which identifies him as the traitor that Vito was expecting.

Michael arranges for a series of murders to occur while he is standing as godfather for Connie and Carlo's son:

Don Stracci and his bodyguards are shot by Clemenza with a shotgun as they exit an elevator;
Moe Greene, while having a massage in one of his hotels, is shot in the eye by an unknown assassin;
Don Cuneo, while leaving a hotel, is trapped in a revolving door by Willi Cicci and shot;
Don Tattaglia and a prostitute he is with are gunned down while in bed by Rocco Lampone and another unknown assassin;
Finally, Don Barzini is shot on the steps of a courthouse by Al Neri, who is disguised by wearing his old policeman's uniform.
After the baptism, Tessio believes he and Hagen are on their way to the meeting between Michael and Barzini he has arranged. Instead, he is surrounded by Willi Cicci and other button men. Realizing that Michael has found out about his betrayal, Tessio tells Hagen that his betrayal was just business. Meanwhile, Michael confronts Carlo about Sonny's murder and gets him to admit his role in setting up the ambush. Michael informs Carlo that his punishment is to be excluded from the family business and hands him a plane ticket to exile in Las Vegas. Carlo gets into a car to go to the airport, where he is garroted to death by Clemenza.

Later, Connie confronts Michael, accusing him of Carlo's murder. Kay questions Michael about Connie's accusation, but he refuses to answer. She insists, and Michael lies, assuring his wife that he had no role in Carlo's death. Kay is relieved by his denial, believing it to be true. The film ends with Clemenza and new caporegime Rocco Lampone paying their respects to Michael. Clemenza kisses Michael's hand and greets him as "Don Corleone." Kay is watching – Michael has become the new Godfather.