Henri CharriÃ¨re (Steve McQueen), is a safecracker nicknamed Papillon because of the butterfly tattoo on his chest, is wrongly convicted of murdering a pimp. In 1933 he is sentenced to life imprisonment within the penal system in French Guiana. En route, he meets a fellow convict, Louis Dega (Dustin Hoffman), a forger and embezzler who is convinced that his wife will secure his release. Papillon offers to protect Dega if he will underwrite the former's escape once they reach French Guiana, however, the two eventually develop a friendship.
After defending Dega against a sadistic guard, Papillon escapes into the jungle but is captured and sentenced to solitary confinement. In gratitude, Dega smuggles extra food to Papillon. When the food smuggling is discovered, prison guards cut Papillon's food rations in half, believing that hunger will force him to reveal the name of his benefactor. Though emaciated and half-insane, and reduced to eating insects to survive, Papillon refuses to give up Dega. After two years he is released from solitary confinement, having spent six months in total darkness and on half rations. A grateful Dega, who would not have had any ill feeling toward Papillon if he had told the warden that it was he who arranged the extra food, wants to pay back Papillon, which Papillon states is not necessary. However, Papillon plans another escape with Dega's help. During a medical exam, a fellow inmate offers to secure them a boat on the outside with the help of a man named Pascal. Clusiot (Woodrow Parfrey), who Papillon and Dega long ago befriended, begs to go along, to which Papillon ultimately agrees. Before the escape attempt, Papillon urges Dega to join them stating "now, while you have a chance." Dega declines, still believing that his wife will eventually get him released, which Papillon does not think will ever happen as the prison system now "owns" him.
While recovering in the infirmary, Papillon meets a homosexual orderly named AndrÃ© Maturette (Robert Deman), who insists on joining their escape plot. During the escape, Clusiot is knocked unconscious by a guard, but Dega, sensing an opportunity and reflecting on what Papillon told him, makes a run for it with Papillon and Maturette. The three do escape, Dega seriously injuring his ankle in the process during a high fall. Pascal is waiting for them outside the prison wall and the men escape into the night. The next day in the jungle, Pascal delivers the prisoners to their boat. They discover that the boat is not seaworthy, at the same time discovering that Dega's injury is a fracture. A local trapper (John Quade), who reveals that Pascal has repeatedly cheated prisoners by taking their money and then arranging to have them captured by bounty hunters, has killed the waiting bounty hunters. He refers Papillon to a nearby leper colony, where they obtain supplies and a boat.
After reaching the mainland, the trio are accosted by a group of soldiers. The soldiers open fire. Maturette is shot and captured along with Dega, still crippled by his broken ankle. After evading the soldiers, Papillon lives for a long period with a native tribe; one day he awakes to find they have moved on. He finds they have left behind a small bag of pearls, which they used to barter with western traders. At a police checkpoint, Papillon pays a nun with a pearl to join her entourage and goes with her to a convent. Admitting he is a fugitive but stressing that he is not a murderer, Papillon asks the Mother Superior for refuge, leaving her all his remaining pearls to prove his good faith. She turns him over to the authorities, keeping the pearls. She justifies her actions by stating that if he is guilty of crimes, he has fed the poor with his donation of the pearls; if he is not guilty of crimes, God will watch over him in prison.
As punishment for his escape, Papillon is sentenced to five years in solitary confinement. He has gray hair when released and sees Maturette, who dies a short while later. He later watches the authorities dump Maturette's dead body into shark infested waters. Papillon is moved to the remote Devil's Island, where he reunites with Dega, who has given up all hope of being released with his wife's aid. From a high cliff, Papillon observes that every seventh wave that comes into a small cove rebounds from the rocks and is powerful enough to carry a man out to sea.
Once again urging Dega to join him in escaping, the two men manufacture two floats out of bagged up coconuts. As the two men are about to escape, Dega declines escaping, having settled on Devil's Island a broken man. After embracing Dega, Papillon leaps from the cliff and, grasping his float, is successfully carried out to sea.
A narrator states that Papillon lived the rest of his life in freedom. He outlived the prison, which was later closed. The prison is shown abandoned and overgrown by jungle plants.
Who does Mother Superior say will watch over Papillon in prison?
God