In late summer 1945, guests are gathered for the wedding reception of Don Vito Corleone's daughter Connie (Talia Shire) and Carlo Rizzi (Gianni Russo). Vito (Marlon Brando), the head of the Corleone Mafia family, is known to friends and associates as is known to friends and associates as "Godfather." He and Tom Hagen (Robert Duvall), his adopted son and the Corleone family lawyer, are hearing requests for favors because, according to Italian tradition, "no Sicilian can refuse a request on his daughter's wedding day." One of the men who asks the Don for a favor is Amerigo Bonasera, a successful mortician and acquaintance of the Don, whose daughter was brutally beaten by two young men because she refused their advances; the men received minimal punishment. Amerigo asks the Don to murder the men responsible for hurting his daughter -- The Don is disappointed in Bonasera, who'd avoided most contact with the Don due to Corleone's nefarious business dealings, and only comes to him in a time of need, even though The Don's wife is godmother to Bonasera's shamed daughter. After asking Amerigo to call him Godfather and recognize their friendship, The Don agrees to have his men punish the young men responsible.

Meanwhile, the Don's youngest son Michael(Al Pacino), a decorated Marine hero returning from World War II service, arrives at the wedding and tells his girlfriend Kay Adams (Diane Keaton) anecdotes about his family, informing her about his father's criminal life; specifically a moment where his father helped Johnny Fontaine get out of an unfavorably music contract with the threat of murder. He reassures her that he is different from his family and doesn't plan to join them in their criminal dealings. The wedding scene serves as critical exposition for the remainder of the film, as Michael introduces the main characters to Kay. Fredo (John Cazale), Michael's next older brother, is a bit dim-witted and quite drunk by the time he finds Michael at the party. Sonny (James Caan), the Don's eldest child, is married but he is a hot-tempered philanderer who sneaks into a bedroom to have sex with one of Connie's bridesmaids, Lucy Mancini (Jeannie Linero). Tom Hagen is not related to the family by blood but is considered one of the Don's sons because he was homeless when he befriended Sonny in the Little Italy neighborhood of Manhattan and the Don took him in. Now a talented attorney, Tom is being groomed for the important position of consigliere (counselor) to the Don, despite his non-Sicilian heritage.

Also among the guests at the celebration is the famous singer Johnny Fontane (Al Martino), Corleone's godson, who has come from Hollywood to petition Vito's help in landing a movie role that will revitalize his flagging career. Jack Woltz (John Marley), the head of the studio, denies Fontane the part (a character much like Johnny himself), which will make him an even bigger star. At first Don Corleone reprimands Johnny for whining about his position, but eventually explains to Johnny: "I'm gonna make him an offer he can't refuse."

After the wedding, Hagen is dispatched to Los Angeles to meet with Woltz, but Woltz angrily tells him that he will never cast Fontane in the role. Woltz holds a grudge because Fontane seduced and "ruined" a starlet who Woltz had been grooming for stardom and with whom he had a sexual relationship. Tom leaves. The next morning, Woltz wakes up in his mansion and as he pulls back the sheets he finds himself in a pool of blood and he screams in horror when he discovers the severed head of his beloved & prized $600,000 stud horse, Khartoum, in the bed with him. (A deleted scene from the film implies that Luca Brasi, Vito's top or hitman, is responsible.)

Upon Hagen's return, the family meets with Virgil "The Turk" Sollozzo (Al Lettieri), who is being backed by the rival Tattaglia family. He asks Don Corleone for financing as well as political and legal protection for importing and distributing heroin. Despite the huge profit to be made, Vito Corleone refuses, explaining that his political influence would be jeopardized by a move into the narcotics trade. The Don's eldest son, Sonny, who had earlier urged the family to enter the narcotics trade, breaks ranks during the meeting and asks about Sollozzo's assurances as to the Corleone Family's investment being guaranteed by the Tattaglia Family. After they escort Sollozzo out, Don Corleone, angry at Sonny's dissension in a non-family member's presence, privately rebukes him. Don Corleone then dispatches Luca Brasi to infiltrate Sollozzo's organization and report back with information. Luca gets a meeting with Bruno Tattaglia and Sollozzo, feigning his desire to switch sides because he's unhappy with the Corleones. During the meeting, while Brasi is bent over to allow Bruno Tattaglia to light his cigarette, he is stabbed in the hand by Sollozzo, and is subsequently garroted by an assassin.

Soon after his meeting with Sollozzo, Don Corleone is gunned down in an assassination attempt just outside his office, and it is not immediately known whether he has survived. Fredo Corleone had been assigned driving and protection duty for his father when Paulie Gatto, the Don's usual bodyguard, had called in sick. Fredo proves to be ineffectual, fumbling with his gun and unable to shoot back. When Sonny hears about the Don being shot and Paulie's absence, he orders Clemenza to find Paulie and bring him to the Don's house.

Sollozzo abducts Tom Hagen and persuades him to offer Sonny the deal previously offered to his father. Enraged, Sonny refuses to consider it and issues an ultimatum to the Tattaglias: turn over Sollozzo or face a lengthy, bloody and costly (for both sides) gang war. They refuse, and instead send Sonny "a Sicilian message," in the form of two fresh fish wrapped in Luca Brasi's bullet-proof vest, to tell the Corleones that Luca Brasi "sleeps with the fishes."

Sonny wants to "go to the mattresses" -- set up beds in apartments for Corleone button men to operate out of in the event that the crime war breaks out. Clemenza later takes Paulie and one of the family's hitmen, Rocco Lampone, for a drive into Manhattan. On their way back from Manhattan, Clemenza has Paulie stop the car in a remote area so he can urinate. Rocco shoots Paulie dead; he and Clemenza leave Paulie and the car behind.

Michael visits his father at a small private hospital. He is shocked to find that no one is guarding him. Realizing that his father is again being set up to be killed, he calls Sonny for help, moves his father to another room, and goes outside to watch the entrance. Michael enlists help from Enzo the baker (Gabriele Torrei), who has come to the hospital to pay his respects. Together, they bluff away Sollozzo's men as they drive by. Police cars soon appear bringing the corrupt Captain McCluskey (Sterling Hayden), who punches Michael and breaks his jaw when Michael insinuates that Sollozzo paid McCluskey to set up his father. Just then, Hagen arrives with "private detectives" licensed to carry guns to protect Don Corleone, and he takes the injured Michael home. Sonny responds by having Bruno Tattaglia (Tony Giorgio), the eldest son and underboss of Don Phillip Tattaglia (Victor Rendina), killed (off-camera).

After the back and forth attacks, Sollozzo requests a meeting with the Corleone's which Captain McCluskey will attend as Sollozzo's bodyguard. While the Corleone's are debating what to do, Michael volunteers to go -- he is considered a civilian and can reasonably expect to be safe from danger. Michael's plan is to use his civilian status as a token to get close and kill them both during the meeting. Sonny and the other senior family members tease Michael for suggesting that he commit murder; however, Michael convinces them that he is serious and that killing Sollozzo is the only way to resolve the issues. In addition, police officers are usually off limits for hits -- Michael argues that since McCluskey is corrupt and has illegal dealings with Sollozzo, he is fair game and with their press connections, they can paint a story in a light that plays to the Corleone's favor.

Before the meeting in a small Italian restaurant, McCluskey frisks Michael for weapons and finds him clean. They talk over dinner in italian, where Michael explains that he wants no more attempts on his father's life in exchange for peace. Sollozzo dances around the topic, saying that Michael thinks too much of him -- he doesn't have any control and he can't make any guarantees. Michael then excuses himself to go to the bathroom where he retrieves a planted revolver, and returning to the table, he fatally shoots Sollozzo, then McCluskey. Michael is sent to hide in Sicily, while the Corleone family prepares for all-out warfare with the Five Families (who are united against the Corleones) as well as a general clampdown on the mob by the police and government authorities.

Meanwhile, Connie and Carlo's marriage is disintegrating. They argue publicly over Carlo's suspected infidelity and his possessive behavior toward Connie. By Italian tradition, nobody, not even a high-ranking Mafia don, can intervene in a married couple's personal disputes, even if they involve infidelity, money, or domestic abuse. One day, Sonny sees a bruise on Connie's face and she tells him that Carlo hit her after she asked him if he was having an affair. Sonny tracks down and severely beats up Carlo Rizzi in the middle of a crowded street for brutalizing the pregnant Connie, and threatens to kill Carlo if he ever abuses Connie again. An angry Carlo responds by plotting with Tattaglia and Don Emilio Barzini (Richard Conte), the Corleones' chief rivals, to have Sonny killed.

Later, Carlo has one of his mistresses phone his house, knowing that Connie will answer. The woman asks Connie to tell Carlo not to meet her tonight. The very pregnant and hormonal Connie assaults Carlo; he takes advantage of the altercation to beat Connie in order to lure Sonny out in the open and away from the Corleone compound. When Connie phones the compound to tell Sonny that Carlo has beaten her again, the furious Sonny drives off (alone and unescorted) to fulfill his threat against Carlo. On the way to Connie and Carlo's house, Sonny is ambushed at a highway toll booth and violently shot to death by several carloads of hitmen wielding Thompson submachine guns.
Back in New York City, Don Corleone returns home from the hospital and is distraught to learn that it was Michael who killed Sollozzo and McCluskey and that Sonny is dead. Rather than seek revenge for Sonny's killing, Don Corleone meets with the heads of the Five Families to negotiate a cease-fire. Not only is the conflict draining all their assets and threatening their survival, but ending it 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, as long as it is controlled and not sold to children. At the meeting, Don Corleone deduces that Don Barzini, not Tattaglia, was ultimately behind the start of the mob war and Sonny's death.

In Sicily, Michael patiently waits out his exile, protected by Don Tommasino (Corrado Gaipa), an old family friend. Michael aimlessly wanders the countryside, accompanied by his ever-present bodyguards, Calo (Franco Citti) and Fabrizio (Angelo Infanti). In a small village, Michael meets and falls in love with Apollonia Vitelli (Simonetta Stefanelli), the beautiful young daughter of a bar owner. They court and marry in the traditional Sicilian fashion, but soon Michael's presence becomes known to Corleone enemies. As the couple is about to be moved to a safer location, Apollonia gets into the car and while Michael is still upstairs and proceeds to turn the car on. The car ends up being rigged with a bomb, and the car explodes, taking Apollonia's life. Michael spots one of his bodyguards, Fabrizio, hurriedly leaving the grounds seconds before the explosion, implicating him in the assassination plot.

With his safety guaranteed, Michael returns home. More than a year later, in 1950, he reunites with his former girlfriend Kay after a total of four years of separation -- three in Italy and one in America. He leave out his marriage and now deceased Italian wife, and tells her that he is now working for his father. She is hurt that he waited so long to contact her, and also disappointed that he is now working for his father. Michael has now changed his stance on his family, and says that his father is just like any powerful man -- and that Michael is taking over, and his goal is to make the family completely legitimate in 5 years. He wants for them to get married and have a child, and Kay, still in love with Michael, believes him and accepts.

Two years later, Peter Clemenza (Richard S. Castellano) and Salvatore Tessio (Abe Vigoda), two Corleone Family caporegimes, complain that they are being pushed around by the Barzini Family and ask permission to strike back. Michael denies the request -- he plans to move the family operations to Nevada and after that, Clemenza and Tessio may break away to form their own families. Michael further promises Connie's husband, Carlo, that he will be his right hand man in Nevada, unaware of his part in Sonny's assassination. 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 (Tom Rosqui). Don Vito explains to Hagen that Michael is acting on his advice.

Another a year or so later, Michael travels to Las Vegas and meets with Moe Greene (Alex Rocco), a rich and shrewd casino boss looking to expand his business dealings. After the Don's attempted assassination, Fredo had been sent to Las Vegas to learn about the casino business from Greene. Michael meets with Moe and offers to buy out Greene's stake in the casino as Michael's first move to get his family into Nevada but is rudely rebuffed by Moe. Greene believes the Corleones are weak now and notes that he can secure a better deal from Barzini. As Moe and Michael heatedly negotiate, Fredo sides with Moe. Afterward, Michael warns Fredo to never again "take sides with anyone against the family."

Michael returns home to recollect and plan. In a private moment, Vito explains his expectation that the Family's enemies will attempt to murder Michael by using a trusted associate to arrange a meeting as a pretext for assassination. Vito also reveals that he had never really intended a life of crime for Michael, hoping that his youngest son would hold legitimate power as a senator or governor. Some months later, Vito collapses and dies while playing with his young grandson Anthony (Anthony Gounaris) in his tomato garden. At the burial, Tessio conveys a proposal for a meeting with Barzini, which identifies Tessio as the traitor that Vito was expecting.

Michael arranges for a series of murders to occur simultaneously while he is standing godfather to Connie's and Carlo's newborn son at the church: Don Stracci (Don Costello) is gunned down along with his bodyguard in a hotel elevator by a shotgun-wielding Clemenza. Moe Greene is killed while having a massage, shot through the eye by an unidentified assassin. Don Cuneo (Rudy Bond) is trapped in a revolving door at the St. Regis Hotel and shot dead by soldier Willi Cicci (Joe Spinell). Don Tattaglia is assassinated in his bed, along with a prostitute, by Rocco Lampone and an unknown associate. Don Barzini is killed on the steps of his office building along with his bodyguard and driver, shot by Al Neri (Richard Bright), disguised in his old police uniform.

After the baptism, Tessio believes he and Hagen are on their way to the meeting between Michael and Barzini that he has arranged. Instead, he is surrounded by Willi Cicci and other button men as Hagen steps away. Realizing that Michael has uncovered his betrayal, Tessio tells Hagen that he always respected Michael, and that his disloyalty "was only business." He asks if Tom can get him off for "old times' sake," but Tom says he cannot. Tessio is driven away and never seen again.

Meanwhile, Michael confronts Carlo about Sonny's murder and forces him to admit his role in setting up the ambush, having been approached by Barzini himself. Michael assures Carlo he will not be killed, but his punishment is exclusion from all family business. He hands Carlo a plane ticket to exile in Las Vegas. However, when Carlo gets into a car headed for the airport, he is garroted to death by Clemenza, on Michael's orders.

Later, a hysterical Connie confronts Michael at the Corleone compound as movers carry away the furniture in preparation for the family move to Nevada. She accuses him of murdering Carlo in retribution for Carlo's brutal treatment of her and for Carlo's suspected involvement in Sonny's murder. After Connie is removed from the house, Kay questions Michael about Connie's accusation, but he refuses to answer, reminding her to never ask him about his business or what he does for a living. She insists, and Michael outright lies, reassuring his wife that he played no role in Carlo's death. Kay believes him and is relieved. The film ends with Clemenza and new caporegimes Rocco Lampone and Al Neri arriving and paying their respects to Michael. Clemenza kisses Michael's hand and greets him as "Don Corleone." As Kay watches, the office door is closed. Michael is the new Godfather.