In 1901, in the village of Corleone, Sicily, nine-year-old Vito Andolini is comforted by his mother as they walk in his father's funeral procession. When shots ring out, Vito's older brother Paolo is killed, prompting Signora Andolini to take Vito to see local Black Hand leader, Don Francesco, called "Ciccio," whom her husband had offended. She begs him to spare Vito's life, but the don coldly refuses, prompting Vito's mother to take a knife to Ciccio's throat and scream for her son to run. She is killed by the don's henchmen, but Vito escapes. Despite threats from Ciccio's men, some villagers help Vito, enabling him to sail to America. When he is diagnosed with smallpox and placed in quarantine on Ellis Island, Vito, who has been given the surname Corleone by an immigration official, gazes at the Statue of Liberty from his small room.
In 1958, Vito's grandson, Anthony Corleone receives his First Holy Communion in Lake Tahoe, Nevada. After the ceremony, his parents, Kay and Michael, host a lavish party at their lakeside estate. Michael, who has succeeded Vito as the don of the Corleone family, receives guests who seek his favor, including Senator Pat Geary, a pompous hypocrite, who incurs Michael's enmity when he demands money in exchange for the license Michael seeks for a gambling casino. Others at the party include Michael's weak, older brother, Fredo, who cannot control his drunken wife, and their widowed younger sister, Connie, who prefers the high life to caring for her children. Al Neri, who represents elderly Jewish gangster Hyman Roth, discusses a Cuban casino deal between Roth and the Corleones, while old family friend and lieutenant Frankie Pentangeli begs Michael not to do business with Roth or his cohorts, the ruthless New York Rosato brothers. Late that night, as Michael prepares for bed and admires a picture that Anthony has drawn for him, the room is riddled by machine gun fire. Because Michael drags himself to Kay's side and covers her body with his, neither is hurt, but Kay is quietly resentful and views Michael's promises to turn the family business legitimate as lies. Michael warns his security men to capture the assassins alive, but by the time the men are found near the lake, they have been killed. Privately, Michael confides in his adopted brother, Tom Hagen, that he is the only person he trusts and relates that he will be in complete charge while Michael goes away to try to solve what has happened.
In 1917, In New York's Little Italy, Vito, now a grown man with a wife and baby son, goes to an Italian-language vaudeville show with his friend, Genco Abbandando, who is in love with one of the actresses. Backstage, Vito sees local Black Hand leader Fanucci intimidate the young actress' father and is distressed to learn that Fanucci offers "protection" to all of the local Italian merchants, even Genco's father, for whom Vito works. Soon after, Clemenza, a neighbor across the alley, throws a package to Vito and asks him to hide it. A short time later, Fanucci comes into the Abbandando grocery and demands that Genco's father hire his nephew. When the distraught Signor Abbandando tells Vito that he must let him go, Vito comforts him and says that he will never forget all of his kindnesses. The next day, Clemenza stops Vito on the street and asks about the package, which contained guns. Impressed when Vito says that he does not concern himself with things that are not his business, Clemenza offers to give Vito's wife a rug that belongs to a friend. Cemenza then takes Vito with him to a luxurious house, where they break in and steal an expensive carpet.
After leaving Lake Tahoe, Michael travels to Miami, where he goes to the modest suburban home occupied by Roth and his wife, and tells him that Pentangeli was behind the assassination attempt. Agreeing to do business together in Cuba, Roth tells Michael to bring $2,000,000 cash to him in Havana. Michael asks Roth if he minds that Pentangeli must be killed, but Roth dismisses Pentangeli as "small potatoes." Next, Michael travels to Long Island, to his father's former house in Long Beach, now occupied by Pentangeli and his family. He then tells Pentangeli that he knows it was Roth who tried to have him killed and asks him to pretend to make peace with the Rosato brothers so that Roth will be lulled into a sense of security. Sometime later, when Pentangeli and his cohort, Willy Cicci, go to a New York bar to meet with the brothers, Tony Rosato grabs him from behind and, saying “Michael Corleone says hello,” starts to strangle him. Just then, a policeman enters the bar and the Rosatos flee, leaving Pentangeli for dead and wounding Cicci outside. Meanwhile, as Michael travels to Cuba, Kay begins to feel like a prisoner at the estate because the guards, under Tom and Michael’s orders, prevent her from leaving. In Havana, Michael and Roth are among several prominent American corporate executives who are being wooed by the country’s president, who assures them that the country’s rebels will be driven out by the new year. Later, on the way to Roth’s 67th birthday party, Michael sees a mass arrest and is struck by the dedication the rebels show when one man blows up himself and a soldier with a grenade. At the party, Roth, who has a heart condition, tells those gathered that he will leave most of his interests to Michael, then privately asks Michael why the $2,000,000 has not arrived. Back at his hotel room, Michael greets Fredo, who has brought a briefcase filled with the money. After Michael tells Fredo that Roth and his underling, Johnny Ola, are in Havana, Fredo denies having met them. Michael then suggests that they spend the day together. Listening as Fredo almost tearfully asks why they never spent time alone together before, Michael, who thinks that Pentangeli has been killed on Roth’s orders, says that Roth will never see the New Year. That night, which is New Year’s Eve, Fredo acts as host to a number of American VIPs, including Sen. Geary, who now is indebted to the Corleone family because a few weeks before, Tom had covered up the violent death of a prostitute with whom Geary was involved. When Johnny arrives, he and Fredo pretend not to know each other, but when the party goes to a sex show and Fredo casually tells Geary and the others that Johnny had told him about the club, Michael knows that Fredo had betrayed him. Meanwhile, Johnny is strangled in his hotel room. The killer then goes to kill Roth, but because Roth has had a mild stroke, he is being taken to the hospital. There, while one of the nurses leaves to celebrate the New Year with her friends, the killer sneaks into Roth’s room and starts to strangle him, but is interrupted by the nurse and a guard, who kills him before he can finish. At midnight, in the presidential palace, Michael embraces Fredo and tells him he knows that it was he who betrayed him and that he broke his heart. Moments later, the president announces that, because the rebels have advanced, he is resigning and will be leaving the country immediately. As Fredo wanders through the chaos in the streets, Michael calls for him to come with him to a waiting plane, but the frightened Fredo runs away. Days later, Michael meets Tom at a Las Vegas hotel and learns that Kay has had a miscarriage. He tells Tom to find Fredo and tell him that he knows he was misled by Roth but he should come home and not be afraid.
In 1918, as Vito drives through Little Italy, Fanucci jumps on his car and tells him that he wants him and his friends to “wet my beak” and give him $200 as part of their earnings from stealing expensive dresses. That night, Vito convinces Clemenza and their friend Tessio to give him $50 and promises to make Fanucci accept that. When Vito visits Fanucci at a local café, he offers the $100, saying he needs more time for the rest. Impressed with Vito’s courage, Fanucci agrees, and leaves. Because it is the Festa of San Rocco, Fanucci struts through the crowds and offers money to the church. Unknown to him, Vito has followed him on the rooftops and enters Fanucci’s house. When Fanucci arrives, Vito shoots him at close range, then takes the money from his wallet, disposes of the pieces of the gun in different drain pipes, then joins his wife and three young sons to watch fireworks.
When Michael returns to his Lake Tahoe estate, he goes to his mother’s cottage to talk with her before his family. Speaking in Italian, he asks if his father ever lost his family. When she says that you never lose your family, he whispers “ tempi cambi ,” times change. At the same time, Willy Cicci, who was only wounded by the Rosato brothers, is testifying before a U.S. Senate committee investigating organized crime, saying that he was a “button man” for Michael when he wanted something done.
In Little Italy, in 1923, Vito is now known as “Don Vito,” and with his old friend Genco, he has started the Genco Olive Oil Company, which imports oil from Sicily. Vito is so respected and feared within the Italian-American community that when his wife’s widowed friend, Signora Colombo, faces eviction by her landlord, Signor Roberto, the mere knowledge that Vito is her patron, makes the frightened Roberto allow her to keep the dog her son loves and stay in her apartment with a lowered rent.
When Michael is summoned to testify at the Senate hearings, rather than exercise his Fifth Amendment rights against self-incrimination, Michael calmly answers the senator’s questions, saying that he is not a Mafia boss but a legitimate businessman. In a statement, Michael challenges them to produce any evidence of his crimes. A short time later, Michael and Tom learn that Pentangeli survived the attack against him and, thinking that Michael had ordered his death, has been cooperating with the FBI. Michael asks Fredo for information, but Fredo, who knows nothing, lashes out at Michael for relegating his older brother to menial assignments. After Michael says that that is what their father wanted, he tells Fredo that he now means nothing to him and never wants to see him again. After leaving Fredo, Michael tells one of his underlings that he doesn’t want anything to happen to Fredo while his mother is alive. Meanwhile, Pentangeli, who is living in comfort within FBI custody, fears testifying, but his FBI guards assure him that they can protect him. When the hearings resume, Pentangeli, who is set to testify, is stunned when he sees his older brother, who lives in Sicily, enter the chambers with Michael. When questioning begins, instead of corroborating what he had said in sworn statements to the FBI, Pentangeli denies Michael’s criminal activity and says that he merely told the FBI what they wanted to hear. Although the senators suspect intimidation, there is nothing they can do. After the hearings, at their Washington hotel, Kay tells Michael that she is leaving him and taking the children with her. While they are arguing, Michael tells her that he knows that she blames him for the miscarriage but that he will change. She then confesses that it was not a miscarriage but an abortion because the “Sicilian thing” must end and she did not want to bring another of his sons into the world. After slapping her with such force that she falls, Michael screams that she will never take his children from him.
In 1927, Vito, his wife and their three young children arrive in Corleone. They are welcomed by Vito’s old friend and now business partner in Genco Olive Oil, Don Tommasino. After celebrating with relatives, who admire the prosperous family, Vito accompanies Tommasino to now elderly Don Ciccio’s estate. After introducing himself and kissing Ciccio’s hand, Vito tells him that his father was Antonio Andolini, then rips the don’s belly apart with his knife. As Ciccio screams out and dies, Tommassino is wounded as he and Vito make their escape. Leaving Corleone a short time later, Vito shows baby Michael how to wave goodbye.
At Mama Corleone’s funeral in Lake Tahoe, a distraught Fredo wants to speak with Michael, but Tom tells him Michael will not enter until Fredo leaves. Connie then goes to speak privately with Michael and tells him that she had hated him for a long time, but now realizes that he was just being strong for the family. Saying that she now wants to take care of him, she asks him if he can forgive Fredo. Michael then goes to Fredo and embraces his sobbing brother, but with his eyes, lets his underling Rocco Lampone know that his feelings have not changed. Sometime later, as Michael and Tom discuss the fact that Roth, who survived a stroke, has been deported from Israel and is flying back to Miami, Michael lashes out at him for not being with him on the things he needs to do. Tom assures him of his loyalty and asks what he can do. Tom soon visits Pentangeli in custody. Assured by Tom that his brother is safely back in Sicily and his own family will be well cared for, Pentangeli, who loves history, lets Tom know that he will die as disgraced Roman senators did, opening their veins in a warm bath. Back in Lake Tahoe, Fredo, who has enjoyed spending time fishing with Anthony is about to go out onto the lake when Connie says that Michael wants Anthony right away. Later, when Fredo and Rocco are out on the lake, Fredo says a “Hail Mary” just before Rocco shoots him. At the same time, Roth arrives at the Miami airport, where he is shot and killed, and the FBI agents discover that Pentangeli has killed himself in the bathtub. As Michael sits alone in his den, he thinks about Pearl Harbor Day, 1941, when he, his brothers and Connie waited for their father to come home for a birthday celebration: Although he is going to college, Michael announces that he has just enlisted in the Marines, angering Sonny and Tom. When their father comes home, everyone leaves the dining room to greet him at the door, except Michael, who remains at the table, alone.