In the Sicilian countryside, Michael is being protected by Don Tommasino (Corrado Gaipa), Corleone's partner in the olive-oil import business, and he is closely watched by bodyguards because Santino (Sonny) has informed them from New York: "Your enemies know you're here." He is struck by the beauty of one of the peasant girls Apollonia (Simonetta Stefanelli), described by one of his bodyguards: "I think you got hit by the thunderbolt." At a cafe, Michael tells her father Vitelli (Saro Urzi) that he meant no disrespect or offense to him or to his daughter when describing her beauty:

I apologize if I offended you. I am a stranger in this country. And I meant no disrespect to you, or your daughter. I am an American, hiding in Sicily. My name is Michael Corleone. There are people who'd pay a lot of money for that information. But then your daughter would lose a father instead of gaining a husband. I wanna meet your daughter with your permission and under the supervision of your family with all respect.

After being permitted an introduction to her at Vitelli's home, Michael presents a gift of a necklace to Apollonia and they quickly develop a romantic friendship.

Back in the US, Sonny unleashes his passions against his brother-in-law Carlo for beating his sister Connie. Connie tries to take the blame for her bruised face, fearing that Sonny's volatile nature will lead to a violent assault on Carlo:

Connie: It was my fault!...Sonny, please it was my fault, Sonny it was my fault. I hit him. I started a fight with him. Please let me be. I hit him so he hit me...Sonny, please don't do anything. Please don't do anything.
Sonny: OK. What's the matter with you? What am I gonna do? I'm gonna make that baby an orphan before he's born or what? Huh? Hmmm? (Connie laughs.) All right?

Soon after, Sonny finds Carlo on a city stoop and mercilessly beats him, punches and kicks him, bites his knuckles, and repeatedly slams a garbage can lid down on his head. Exhausted, he threatens: "You touch my sister again. I'll kill ya," and as he leaves, he kicks Carlo one last time. He leaves Carlo motionless on his back in the downpour of an open fire hydrant.

In a village church in Sicily, Michael marries Apollonia in a traditional Sicilian wedding ceremony, followed by dancing at the reception in the village square. In the privacy of their bedroom on their wedding night, the beautiful young bride removes her silky slip and reveals her breasts to him before they consummate their love (off-screen). Kay, Michael's previous girlfriend, arrives in a cab at the Corleone main gate, asking Tom for Michael's whereabouts. Tom can only tell her: "Nobody knows where he is. We know that he's all right, but that's all." In the wake of violent bloodbath massacres of the Corleones and rival gang members, family violence also escalates. After learning about one of no-good husband Carlo's "whore" girlfriends, Connie smashes every dish in sight in their home. Bullying his wife, Carlo whips Connie with his belt to "clean it up" and then taunts her when she grabs a knife: "Yeah, yeah, come on now, kill me. Be a murderer like your father. Come on, all you Corleones are murderers anyway." She threatens to kill him, but he retaliates with his superior strength and beats her senseless: "Go 'head, now I'll kill you. You guinea brat you. Get out here." In a barely audible voice, Connie phones Sonny after this latest attack. Volatile, Sonny is incensed and leaves to get revenge on Carlo - the "Sonofabitch," but he blunders into a trap that costs him his life.

The most violent scene in the film is the spectacular ambush and machine gun assassination at the tollbooths located at Point Lookout on the Jones Beach Causeway. After the tolltaker in the causeway ducks below the window, Sonny is ambushed and massacred by carloads of gangsters with machine guns and a merciless fusillade of bullets.

[According to the film's own chronological sequence, the murder scene occurs at the end of 1948 or early in 1949. However, the audio on Sonny's radio is playing Russ Hodges' call (on WMCA radio, 570 on the dial) of the moments before NY Giants player Bobby Thomson hit a 3-run home run against Dodger pitcher Ralph Branca. "The shot heard 'round the world" wins the 1951 National League pennant for the Giants (in a best of three playoff series). With a 0-1 count, and with the Brooklyn Dodgers leading 4-2, he pounded the ball deep to the lower deck of the left field stands to beat the Dodgers at the Polo Grounds in New York City - precisely pinpointing the date as October 3, 1951.]

Sonny's assassins unnecessarily kick his corpse after he's been shot and killed. [Weak-willed Carlo has betrayed Sonny and set him up for a "hit" by rival Mafia chief Barzini (Richard Conte).] In response to the killing, Don Corleone bows his head - he is physically shaken and weakened:

I want no inquiries made. I want no acts of vengeance. I want you to arrange a meeting, with the heads of the Five Families. This war stops now.

At his funeral parlor, undertaker Bonasera is asked to repay the earlier favor of justice by offering his friendship and "service" to Corleone: "I want you to use all your powers and all your skills. I don't want his mother to see him this way. Look how they massacred my boy." Bonasera has the impossible task of cosmetically restoring and covering up Sonny's massacred, bullet-riddled corpse and mangled, ravaged face so that his mother can look at him (and not see what death has done to him).

Michael's rival-gang enemies learn of Michael's whereabouts and plant a bomb in his car in their villa courtyard, with help in the set up by his bodyguard Fabrizio. Michael senses that the car is rigged with explosives and that the Sicilian bodyguard has disappeared - as Appolonia prepares to start the car. His expressions register his insight, but he cannot save his wife's life. It is not Michael but Apollonia, his young Italian wife and soulmate, who is brutally killed by the explosion intended for her husband.

A meeting of the heads of the Five Families and associates - from upper New York State, New Jersey and Manhattan's West Side docks, the Bronx, and Staten Island (Barzini and Tattaglia are both dons there), including twelve principals, is held in a downtown city boardroom. Corleone is the head of the Sixth Family. Debate first centers around Corleone's refusal to allow drug trafficking and share "all the judges and the politicians" in New York. Corleone wishes to end the endless months of slaughter and is reluctantly willing to compromise and allow narcotics operations:

Corleone: How did things ever get so far? I don't know. It was so unfortunate, so unnecessary. Tattaglia lost a son and I lost a son. We're quits. And if Tattaglia agrees, then I'm willing to let things go on the way they were before.
Barzini: We're all grateful to Don Corleone for calling this meeting. We all know him as a man of his word. A modest man who will always listen to reason.
Tattaglia: Yes, Barzini, he is too modest. He had all the judges and politicians in his pocket and refused to share them.
Corleone: When, when did I ever refuse an accommodation? All of you know me here. When did I ever refuse, except one time? And why? Because I believe this drug business is gonna destroy us in the years to come. I mean, it's not like gambling or liquor, or even women, which is something that most people want nowadays and is forbidden to them by the pezzonovante of the church. Even the police departments that have helped us in the past with gambling and other things are gonna refuse to help us when it comes to narcotics. And I believed that then - and I believe that now.
Barzini: Times have changed. It's not like the old days when we could do anything we want. A refusal is not the act of a friend. Don Corleone had all the judges and the politicians in New York and he must share them...He must let us draw the water from the well. Certainly, he can present a bill for such services. After all, we are not Communists...
Corleone: I hoped that we could come here and reason together. And as a reasonable man, I'm willing to do whatever's necessary to find a peaceful solution to these problems.
Barzini: Then we are agreed. The traffic in drugs will be permitted, but controlled, and Don Corleone will give up protection in the East - and there will be the peace.
Tattaglia: But I must have strict assurance from Corleone. As time goes by and his position becomes stronger, will he attempt any individual vendetta?
Barzini: Look, we are all reasonable men here. We don't have to give assurances as if we were lawyers.
Corleone: You talk about vengeance. Is vengeance gonna bring your son back to you? Or my boy to me? I forego the vengeance of my son. But I have selfish reasons.

Corleone also announces his intention to make arrangements to bring his youngest son Michael back safely, but warns:

My youngest son was forced to leave this country because of this Sollozzo business. All right. And I have to make arrangements to bring him back here safely, cleared of all these false charges. But I'm a superstitious man. And if some unlucky accident should befall him - if he should get shot in the head by a police officer, or if he should hang himself in his jail cell, or if he's struck by a bolt of lightning - then I'm going to blame some of the people in this room. And that I do not forgive. But that aside, let me say that I swear on the souls of my grandchildren, that I will not be the one to break the peace that we've made here today.

From their short meeting, Corleone perceptively understands that Barzini had backed Sollozzo and Tattaglia from the very beginning: "I didn't know till this day that it was Barzini all along." Following news of Sonny's death and the death of his own wife in late 1948 or early 1949, Michael returns home as the new, hardened Don, heir successor to his father. After being home for a year, Michael aggressively pursues ex-fiancee Kay at a school in New Hampshire where her parents live and where she teaches schoolchildren:

Michael: I'm working for my father now. He's been sick, very sick.
Kay: But you're not like him, Michael. I thought you weren't going to become a man like your father. That's what you told me.
Michael: My father's no different than any other powerful man (Kay laughs), any man who's responsible for other people. Like a senator or a president.
Kay: You know how naive you sound?
Michael: Why?
Kay: Senators and presidents don't have men killed.
Michael: Oh, who's being naive, Kay? Kay, my father's way of doing things is over, it's finished. Even he knows that. I mean in five years, the Corleone Family is going to be completely legitimate. Trust me. That's all I can tell you about my business.

Michael asks her to marry him and promises that he will go legitimate in five years. Kay objects that "it's too late," but Michael persuades her that they can "have a life together...have children, our children" - they marry in 1951.

By 1952, Michael has taken over more and more of the business, with the Don's permission, planning to expand his family's operations (legal gambling, prostitution, and narcotics) into Nevada (Las Vegas), with Carlo serving as his "right-hand man," and Tom Hagen as "our lawyer in Vegas" - no longer consigliere. Hagen asks why he is "out" and is told: "You're not a wartime consigliere, Tom. Things may get rough with the move we're trying."

In Vegas, where the roadways are decorated with signs for casinos and entertainment shows (Patti Page, Joe E. Lewis and Gloria De Haven, and Dean Martin and Jerry Lewis), Michael visits with his brother Fredo and Johnny Fontane. He rejects his brother's studly attempts to impress him with a welcoming party, band, and women. Michael explains how the Corleone Family is changing its interests:

The Corleone Family is thinking of giving up all its interests in the olive oil business and settling out here. Now Moe Greene will sell us his share of the casino and the hotel so it could be completely owned by the Family...I'll make him an offer he can't refuse.

As a favor to the family after intervening with Woltz, Michael requests that Johnny Fontane sign a contract, promising to make five singing appearances each year at the casino owned by the Corleone family and to "perhaps convince some of your friends in the movies to do the same." But hotel/casino owner Moe Greene (Alex Rocco) insults Michael, refusing to be given orders and to be taken over and bought out:

You god-damn guineas really make me laugh...Yeah, let's talk business, Mike. First of all, you're all done. The Corleone Family don't even have that kind of muscle anymore. The Godfather's sick, right? You're getting chased out of New York by Barzini and the other Families. What do you think is going on here? You think you can come to my hotel and take over? I talked to Barzini. I can make a deal with him and still keep my hotel...Sonofabitch, do you know who I am? I'm Moe Greene. I made my bones when you were going out with cheerleaders!

After Greene has left, Fredo blasts his brother: "Mike! You don't come to Las Vegas and talk to a man like Moe Greene like that!" Michael reprimands Fredo for opposing Family interests and supporting Greene (as Sonny had done earlier): "Fredo, you're my older brother, and I love you. But don't ever take sides with anyone against the Family again. Ever."

Returning to the East Coast, Michael has a few words with his wise, aging father in the outdoor garden. They are affectionate to each other, but cannot express their emotions openly. While drinking wine, Corleone offers his own thoughts about Michael's succession and his hopes for his son. He also suggests his perceptions about "this Barzini business":

Barzini will move against you first. He'll set up a meeting with someone that you absolutely trust, guaranteeing your safety. And at that meeting, you'll be assassinated...It's an old habit. I spend my life trying not to be careless. Women and children can be careless, but not men...It could be anyone...I never, I never wanted this for you. I worked my whole life - I don't apologize, to take care of my family. And I refused to be a fool dancing on a string held by all those - big shots. I don't apologize; that's my life. But I thought that...when it was your time that - that you would be the one to hold the strings...This wasn't enough time, Michael, it wasn't enough time...Now listen, whoever comes to you with this Barzini meeting, he's the traitor. Don't forget that.

In a vivid death scene among the tomato plants in 1954, the Don plays with Michael's three year old son Anthony, his grandchild. He teaches Anthony how to use a spray can, and then scares him by putting a sliced piece of orange peel in his mouth and pretending to be a grotesque boogey monster. [The suggestion is that he is a monster underneath his grandfatherly figure.] He comforts his frightened grandson in his arms. While running with the boy in the garden, the Don suffers a fatal heart attack. His funeral is attended by family mourners and rival gang member Barzini. Following the service, turncoat Sal Tessio whispers in Michael's ear that "Barzini wants to arrange a meeting (to) straighten any of our problems out."

In the final extraordinary baptism scene, probably occurring in 1955, Michael acts as godfather at the christening of his sister Connie's (and Carlo's) child, his nephew and namesake. [The infant in the scene is director Coppola's daughter Sofia Coppola in an uncredited role.] The scene brilliantly crosscuts back and forth from the church to locations throughout the city as gangland murders are orchestrated. With controlled intensity, Michael engineers a cold-blooded mass killing of Barzini, Tattaglia, Greene and all other rival gangleaders of the Five Families to settle the "Family business." While methodically committing the series of vicious and bloody counterattack murders to confirm his position as the new godfather, he is at the church altar listening to holy recitations of the priest during the baptism - in juxtaposed scenes. He targets each of the Dons of the other leading Families in New York, plus a mobster in Las Vegas.

The killings take place in the following order:

• Clemenza kills Don Victor Stracci and an associate as they emerge from an elevator in the St. Regis Hotel
• As Michael renounces Satan at the baptism ceremony, in a massage and sun lamp room in Las Vegas, Moe Greene is shot through the eye (through his black-rimmed glasses) by an unknown assailant - blood drips down his face from behind the shattered lens
• Willy Cicci (Joe Spinell) kills Don Carmine Cuneo (Rudy Bond) trapped in a revolving door in the front of the St. Regis Hotel
• Rocco Lampone and another man machine gun Philip Tattaglia (Victor Rendina) and a 'whore' naked in bed
• Posing as a New York cop, Al Neri kills Barzini's bodyguard (with two shots), Barzini's chauffeur (with another shot), and Barzini himself (with three shots in the back as he flees up a flight of stairs)

Betrayer Tessio realizes that he has been found out for his part in setting up Michael. He asks Tom for an impossible pardon:

Tell Mike it was only business. I always liked him...Tom, can you get me off the hook? For ol' times' sake?

He is eliminated, off-camera, by Willy Cicci. At Connie and Carlo's house, Michael tells his brother-in-law: "You have to answer for Santino, Carlo...You fingered Sonny for the Barzini people. Ahh, that little farce you played with my sister. You think that could fool a Corleone?" He persuades Carlo to confess that it was Barzini who paid him to set Sonny up:

Michael: Come on. Don't be afraid, Carlo. Come on, you think I'd make my sister a widow? I'm Godfather to your son, Carlo...You're out of the Family business, that's your punishment. You're finished. I'm putting you on a plane to Vegas...I want you to stay there, understand? Only don't tell me you're innocent. Because it insults my intelligence and makes me very angry. Now, who approached you? Tattaglia or Barzini?
Carlo: It was Barzini.
Michael: Good.

Clemenza is ordered to murder Carlo in a brutal and painful manner - strangling him from behind while inside a car bound for the airport. Carlo valiantly kicks a hole through the car windshield as he tries to break free while being choked to death.

The ending scene of the film is justifiably famous. As the house is vacated and furnishings are moved by packers to their new home in Nevada, Connie hysterically accuses Michael of being responsible for her treacherous husband's death. She calls Michael a "lousy, cold-hearted bastard." Kay, Michael's non-Italian wife, asks whether Connie's accusation is true about the order to kill their brother-in-law. Denying responsibility, Kay is patronizingly lied to about his business:

Kay: Michael, is it true?
Michael: Don't ask me about my business, Kay.
Kay: Is it true?
Michael: Don't ask me about my business...
Kay: No.
Michael (slamming his hand on the desk): Enough. All right. This one time, this one time I'll let you ask me about my affairs.
Kay (whispering): Is it true? Is it?
Michael (quietly, shaking his head): No.
Kay (sighing relief): (Michael kisses and hugs her.) I guess we both need a drink, huh?

She leaves his study to fix a drink, shaky but smiling. At the same time, family henchmen Rocco Lampone, Clemenza and Al Neri (known as Michael's 'Luca Brasi') enter Michael's study, telling him of the successful assassinations of his enemies and betrayers, and paying tribute. Kay stares at them in the study - Clemenza embraces Michael, shaking and kissing his hand, clearly anointing him as the new Don Corleone of the Family: "Don Corleone." Rocco is the second one to kiss his ring hand. [The Godfather, Part II (1974) begins with this shot.] Michael has emerged as the new Godfather in his father's image, an image he once sought to escape.

Symbolically, the door in Michael's office is shut on Kay by Neri. The door blocks and excludes her view - rubbing her out of the heart of his life and clearly delineating the two worlds. The screen turns to black as the ending credits begin to scroll.