The film I’m Not There is inspired, as the credits say, "by the music and many lives of Bob Dylan." We see a POV shoot of a performer walking out on a stage at his concert to perform, then it cuts to him riding his motorcycle just before he crashes, just as Dylan did in 1966. We see the crash victim is Jude Quinn (Cate Blanchett), who has an autopsy performed on him.
In 1959, a 12-year-old African-American boy (Marcus Carl Franklin) is riding the rails as a hobo. He meets two older hobos and introduces himself as Woody Guthrie. Woody carries around a guitar labeled "This Machine Kills Fascists" as did the real Woody Guthrie. Woody is traveling across country to fulfill his dream to be a singer.
Woody tells the other hobos his life story. He once tried to perform with a circus but is made fun of and kicked out for unknown reasons (although wrestler Gorgeous George gives him a hand). Woody later meets and befriends an African-American family where he stays at their home to be cared for; he also sings "Tombstone Blues" with two of the men. Woody later has dinner with the family where he is lectured by the family matriarch. She reminds him of the goings on of the world and tells Woody, "Live your own time child, sing about your own time." Later that night Woody leaves the home and a note thanking the family for their hospitality and hops aboard a freight train.
Later that night he falls asleep and is awakened by thieves who are looking for money and attempt to rob Woody, but he gets away by jumping off the train and into a river. He seems to imagine an unknown woman underwater and then seems to see himself getting eaten by a Moby Dick-like sperm whale. A white couple later finds him unconscious and take him to a hospital, with a little water in his lungs, but he survives.
The couple take him into their home to temporarily care for him and he performs "When the Ship Comes In" for them. However, they soon get a call from a juvenile correction center in Minnesota from which Woody had escaped. Woody then leaves the couple's home and takes a train ride (which brings us to the beginning of the story with the other two hobos). He hops off in New Jersey to visit his idol, the real Woody Guthrie, who is slowly dying in a hospital. Woody bring flowers and weeps at Guthrie's beside, and is last seen playing a song for his comatose idol.