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 who is known to friends and associates as "Godfather" and Tom Hagen (Robert Duvall), the Corleone family lawyer and consigliere (counselor), are hearing requests for favors because "no Sicilian can refuse a request on his daughter's wedding day". Meanwhile, the Don's youngest son Michael (Al Pacino), a decorated Marine war hero returning from World War II service, tells his girlfriend Kay Adams (Diane Keaton) anecdotes about his family, attempting to inform her about his father's criminal life; he reassures her that he is different from his family. Among depicting the marriage of Connie and Carlo, the wedding scene also serves as a critical exposition scene for the remainder of the film, as Michael figuratively introduces the main characters to Kay.
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, but Don Corleone explains to Johnny: "I'm gonna 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 and will make him an even bigger star, because Fontane seduced and "ruined" a starlet that Woltz favored. Woltz is persuaded otherwise, however, when he wakes up early the next morning and feels something wet in his bed. He pulls back the sheets, and finds himself in a pool of blood with the severed head of his prized $600,000 stud horse, Khartoum, in the bed with him, and screams in horror. (A deleted scene from the film implies that Luca Brasi, Vito's top "button man" 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, and political and legal protection for importing and distributing heroin. Despite the huge profit to be made, Corleone refuses, explaining that his political influence would be jeopardized by a move into the narcotics trade. The Don's eldest son, hotheaded Sonny (James Caan), who had earlier urged the family to enter into the narcotics trade, breaks ranks 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 a non-family member's presence, privately rebukes him later. Don Corleone then dispatches Luca Brasi (Lenny Montana) to infiltrate Sollozzo's organization and report back with information. During the meeting, whilst Brasi is bent over to allow Bruno Tattaglia to light his cigarette, he is stabbed in his hand to prevent him from defending himself, and is subsequently garroted by an assasin.
Soon after his meeting with Sollozzo, Don Corleone is gunned down in an assassination attempt, and it is not immediately known whether he has survived. 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 war. They refuse, and instead send Sonny "a Sicilian message," in the form of a fresh fish wrapped in Luca Brasi's bullet-proof vest, to tell the Corleones that Luca Brasi "sleeps with the fishes".
Michael, whom the other Mafia families consider a "civilian" uninvolved in mob business, visits his father at the 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, 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 with the corrupt Captain McCluskey (Sterling Hayden), who breaks Michael's jaw when he 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 Michael home. Sonny responds by having Bruno Tattaglia, son and underboss of Don Phillip Tattaglia (Victor Rendina), killed.
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. When Michael volunteers to kill both men during the meeting, Sonny and the other senior Family members are amused; 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 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.
Before the meeting in an Italian restaurant, McCluskey frisks Michael for weapons and finds him clean. Michael 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.
Sonny severely beats Carlo Rizzi for brutalizing the pregnant Connie, and threatens to kill him if he ever abuses his sister again. An angry Carlo responds by plotting with Tattaglia and Don Emilio Barzini (Richard Conte), the Corleones' chief rivals, to have Sonny killed. Carlo again beats Connie in order to lure Sonny out. Furious, Sonny drives off alone to fulfill his threat. On the way, he is ambushed at a toll booth and shot to death in his car.
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 it draining all 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, 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 mob war and Sonny's death.
In Sicily, Michael patiently waits out his exile, protected by Don Tommasino, an old family friend. Michael aimlessly wanders the countryside, accompanied by his ever-present bodyguards, Calo and Fabrizio. In a small village, Michael meets and falls in love with Apollonia Vitelli (Simonetta Stefanelli), the beautiful young daughter of a bar owner. They are soon married, but soon Michael's presence becomes known to Corleone enemies. As the couple is about to be moved to a safer location, Apollonia is killed when their car is bombed; Michael, who barely escapes alive, spots Fabrizio hurriedly leaving the grounds mere seconds before the explosion, implicating him in the assassination plot.
With his safety guaranteed, Michael returns home. More than a year later, he reunites with his former girlfriend Kay after a total of four years, three in Italy, and one in America. He tells her he wants them to be married. Although Kay is hurt that he waited so long to contact her, she accepts his proposal. With the Don semi-retired, Sonny dead, and middle brother Fredo (John Cazale) considered incapable of running the family business, Michael is now in charge; he promises Kay he will make the family business completely legitimate within five years.
Peter Clemenza (Richard S. Castellano) and Salvatore Tessio (Abe Vigoda), two Corleone Family caporegimes (captains) complain that they are being pushed around by the Barzini Family and ask permission to strike back, but 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. 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.
In Las Vegas Michael meets with casino boss Moe Greene (Alex Rocco). 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. 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. 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. Shortly after, Vito collapses and dies while playing with his young grandson Anthony 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 is gunned down along with his men in an elevator by Clemenza. Moe Greene While having a massage, he is shot through the eye by an unknown assassin. Don Cuneo is trapped in a revolving door and shot dead by Willi Cicci. Don Tattaglia is assassinated in his bed, along with a prostitute, by Rocco Lampone and an unknown associate. Don Barzini, along with his bodyguard and driver, are shot by Al Neri, 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. Meanwhile, Michael confronts Carlo about Sonny's murder and forces him to admit his role in setting up the ambush. Michael assures Carlo he will not be killed, that 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, accusing him of murdering Carlo. Kay questions Michael about Connie's accusation, but he refuses to answer, reminding her to never ask him about his business. She insists, and Michael 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 paying their respects to Michael. Clemenza kisses Michael's hand and greets him as "Don Corleone." As Kay watches, the door is closed. Michael is the new Godfather.
1945年夏天，美国本部黑手党科莱昂家族首领，“教父”维托·唐·科莱昂为小女儿康妮举行了盛大的婚礼。“教父”有三个儿子：好色的长子逊尼，懦弱的次子弗雷德和刚从二战战场回来的小儿子迈克。其中逊尼是“教父”的得力助手;而迈克虽然精明能干，却对家族的“事业”没什么兴趣。
“教父”是黑手党首领，常干违法的构当。但同时他也是许多弱小平民的保护神，深得人们爱戴。他还有一个准则就是决不贩毒害人。为此他拒绝了毒枭素洛佐的要求，并因此激化了与纽约其它几个黑手党家族的矛盾。圣诞前夕，素洛佐劫持了“教父”的大女婿汤姆(电影中未提)，并派人暗杀“教父”。“教父”中枪入院。素洛佐要汤姆设法使逊尼同意毒品买卖，重新谈判。逊尼有勇无谋，他发誓报仇，却无计可施。
迈克去医院探望父亲，他发现保镖已被收买，而警方亦和素洛佐串通一气。各家族间的火并一触即发。迈克制定了一个计策诱使素洛佐和警长前来谈判。在一家小餐馆内，迈克用事先藏在厕所内的手枪击毙了素洛佐和警长。
迈克逃到了西西里，在那里他娶了美丽的阿波萝妮亚为妻，过着田园诗般的生活。而此时，纽约各个黑手党家族间的仇杀却越来越激烈。逊尼也被康妮的丈夫卡洛出卖，被人打得千疮百孔。“教父”伤愈复出，安排各家族间的和解。听到噩耗的迈克也受到了袭击。被收买的保镖法布里奇奥在迈克的车上装了炸弹。迈克虽幸免于难，却痛失爱妻。
迈克于1951 年回到了纽约，并和前女友凯结了婚。日益衰老的“教父”将家族首领的位置传给了迈克。在“教父”病故之后，迈克开始了酝酿已久的复仇。他派人刺杀了另两个敌对家族的首领，并亲自杀死了谋害他前妻的法布里奇奥(电影中貌似没这情节)。同时他也命人杀死了卡洛，为逊尼报了仇。
仇敌尽数剪除。康妮因为丈夫被杀而冲进了家门，疯狂地撕打迈克。迈克冷峻地命人把康妮送进了疯人院(电影中好像没提及)。他已经成了新一代的“教父”——唐·科莱昂