The story starts in the early 1960s with a young Liverpudlian ship builder named Jude (Jim Sturgess) who travels by ship to the United States in search of his American G.I. father, Wes (Robert Clohessy), whom he has never met and who does not know he exists. While searching for his father at Princeton, he befriends Max (Joe Anderson), a rebellious young man from a privileged background, and his sister Lucy (Evan Rachel Wood). Max drops out of college and moves to New York City, accompanied by Jude. Max works as a taxi driver, while Jude pursues work as a freelance artist. They become roommates in a bohemian enclave where they share an apartment with other people, most notably Sadie (Dana Fuchs), their landlady who is an aspiring singer. Other residents include Jojo (Martin Luther McCoy), a guitarist who arrives from Detroit after the death of his younger brother during the 12th Street riot; and Prudence (T.V. Carpio), a bisexual girl who hitchhikes to New York City from Dayton, Ohio. Lucy joins them in New York after her boyfriend is killed in the Vietnam War.
Romances develop between Lucy and Jude, and between Sadie and Jojo, which makes Prudence depressed. When Max is drafted and sent to Vietnam, Lucy becomes involved in a radical anti-war movement, which leads to strains with the comparatively apolitical Jude. He is unhappy with the amount of time she spends with the political group, suspecting that its leader, Paco (Logan Marshall-Green), is a lothario. Jude's art and his relationship with Lucy both start to falter. Meanwhile, Sadie has formed a band, Sadie and the Po Boys, with Jojo as her lead guitarist. She gains the attention of a manager (James Urbaniak) who signs her to a record label, but he wants her to drop her backing band. This causes Sadie and Jojo to break up both musically and romantically.
The differences between Jude and Lucy escalate. One day, Jude storms into the offices of the political group where Lucy works and is kicked out after punching Paco. This leads to a fight between the couple, resulting in Lucy leaving Jude. Jude finds her at an anti-war demonstration at Columbia University during which many protesters, including Lucy, are arrested. In attempting to help her, Jude is also arrested. Though Wes convinces the police not to press charges for actions at the protest, he cannot prove that Jude is his son, and Jude is deported back to England. Max is wounded in Vietnam and is repatriated, emotionally and mentally shattered by his experiences, while Lucy remains involved in her anti-war faction that is becoming more and more violent. She finally leaves the group when she returns to their old headquarters and discovers Paco and some of his followers making bombs. One of their creations explodes, destroying the building. Jude reads about the explosion in a Liverpool newspaper and is concerned that Lucy has died. He subsequently hears from Max that she is alive, and he arranges to return to the States legally. In the end, Jude finds Lucy, and serenades her on a rooftop after the police break up an illegal performance by Sadie and Jojo.