The film begins with Jude (a reference to the song "Hey Jude") singing the beginning verse of "Girl". As the opening credits roll, Sadie and her band are heard singing "Helter Skelter". The scene intercuts sceens of Lucy's prom and Jude's date at the Cavern Club in Liverpool with his girlfriend Molly. "Molly" and "Lucy" are references to the Beatles songs "Ob-la-di, Ob-la-da" and "Lucy in the Sky with Diamonds". Molly and Lucy are both singing "Hold Me Tight". The shipyard payroll clerk says to Jude that he told himself "When I'm Sixty-Four", he was going to be out of this place. "All My Loving" is then sung by Jude to Molly prior to departing for America. When Prudence (referencing the song, "Dear Prudence") appears at football practice at her school in Dayton, singing "I Want to Hold Your Hand", she is thinking of one of the other cheerleaders, which becomes clear as she sings the line, "And let me be your man." When Jude meets Max, (referencing the song "Maxwell's Silver Hammer"), "With a Little Help from My Friends" is sung around the Princeton campus, the college Max attends. Towards the climax of the musical number, the melody for the song transcends to "Dig A Pony" and reverts back to "With A Little Help from My Friends". Lucy sings "It Won't Be Long" when she gets a letter from her boyfriend saying he'll be home before he ships out to Vietnam. At a bowling alley, Jude realizes he has feelings for Lucy, singing "I've Just Seen a Face". Max and Jude rent a New York apartment from a landlady named Sadie, (referencing the song "Sexy Sadie"), who then remarks that Max may have "murdered [his] granny with a hammer", further referencing "Maxwell's Silver Hammer". The scene shifts to show a small child hiding next to a burned out car during the 12th Street riot, singing "Let It Be". The style of the song changes into a gospel rendition behind intercut scenes of the funeral of the boy, who was shot by police in the riot, and that of Lucy's boyfriend, killed in Vietnam.
As Jojo (referencing the song "Get Back") arrives in New York City, Joe Cocker sings "Come Together", switching between playing a bum, a pimp, and a street seller. When Prudence comes into the group's apartment, the lines "Hello Hello" are said in greeting and "She came in through the bathroom window" is said in response to Sadie's questioning her sudden appearance. Later, Sadie sings "Why Don't We Do It in the Road?" at Cafe Huh? (a reference to Cafe Wha? in Greenwich Village). Next, Jude and Lucy are at a dock, and Lucy sings "If I Fell" as she realizes her own feelings toward him. The songs ends with their kiss and embrace at a party. Max is drafted and during his recruitment tests we hear "I Want You (She's So Heavy)"; the scene later shifts to Sadie singing to Jojo and Prudence distantly singing to Sadie through her window. Prudence is heartbroken, locking herself in the closet. Sadie, Max, Lucy, and Jude sing "Dear Prudence" to convince her to come out. Max is later seen fixing a fan with a silver hammer referencing the song "Maxwell's Silver Hammer". "Flying" and "Blue Jay Way" appear in the background shortly thereafter.
Dr. Robert (a reference to the song "Dr. Robert", played by Bono), sings "I Am the Walrus", and the song continues as they drive away on Dr. Robert's bus (a reference to the television film "Magical Mystery Tour"). They find a circus grounds and Mr. Kite (Eddie Izzard) performs "Being for the Benefit of Mr. Kite!" (the song of which his name is derived), accompanied by the Blue Meanies from Yellow Submarine. Reunited with Prudence, who was performing in the circus and is involved with a contortionist named Rita (a reference to the song "Lovely Rita"), they all lie down in a field and sing "Because", then the film moves into a surreal underwater montage.
Back in New York, Jude sings "Something" as he sketches the sleeping naked Lucy. In the apartment, the naked sketches of both Jude and Lucy on the walls are also a reference to the "Two Virgins" album by John Lennon as both appear in similar poses. Next, Sadie and her band sing "Oh! Darling" at a gig at a large venue, leading to Jojo and Sadie's breakup, where Jojo deliberately messes up the guitar and makes Sadie storm out. At some point, Jude is working on a still life drawing of an apple in reference to the Beatles record company. When Jude is working on a logo for Sadie's new record label in his bedroom, tacking strawberries on a board, he (later joined by Max, who is currently in Vietnam) sings "Strawberry Fields Forever". The sequence for this song sometimes resembles parts of the Beatles' promotional video for the song.
Jude bursts in on Lucy at the Students for a Democratic Reformation's office ("Revolution"). After the assassination of Martin Luther King Jr., there is a shift to Jojo, seen in the bar singing "While My Guitar Gently Weeps".
Jude sings "Across the Universe" on the subway on his way to find Lucy at the Columbia University protests of 1968. He continues singing the refrain as the scene shifts between the protest and Sadie in concert singing "Helter Skelter". When Max is in the Stateside hospital, he and other wounded soldiers sing "Happiness Is a Warm Gun." When Lucy is caught in the middle of a violent demonstration, there is a slight reprise of "Revolution". Jeff Beck's version of "A Day in the Life" plays as Jude, back in the Liverpool shipyards, wanders the Liverpool streets. When Max is out of the hospital, Lucy sings "Blackbird" to him.
The scene now shifts between Jude and Max at different bars, and Max begins to sing "Hey Jude" as Jude goes back to New York. Max picks him up from the port and drives him to hear Sadie and Jojo sing "Don't Let Me Down" atop a building, in reference to the last concert of The Beatles, on the rooftop of the Apple Records building in London, where the band played some songs, "Don't Let Me Down" included. Jude then sings "All You Need is Love" a cappella. Max inserts the refrain from "She Loves You", which is doubly a propos, as Paul McCartney sang the line twice himself in a moment of ebullient self-parody during the live recording session for "All You Need is Love" in June of 1967 (audible in the released recording's fade out) - and as Lucy is revealed to be watching Jude sing from a neighboring rooftop.
Over the credits, Bono (with background vocals by The Edge) sings "Lucy in the Sky with Diamonds." "Flying" is reprised in a cover version by The Secret Machines.
