Family man Wade Porter (Stephen Dorff) is living the American Dream with his girlfriend Laura (Marisol Nichols) and their son Michael: they have a nice house, he has just raised a loan to make his company grow and they are going to get married. However their dream becomes a nightmare when Wade unintentionally kills a burglar that had broken into their house in the middle of the night on his lawn. Due to the fact that Wade attacked the intruder and killed him outside of the house, he is tried for murder, and accepts a deal proposed by the prosecutor, being sentenced to three years in prison. In the county jail, Wade gets into a brawl the first night after being attacked by an inmate in the community cell. After his sentencing is given, he is transferred to Corcoran State Prison. On the bus ride over, Danny Sampson, leader of the local Aryan Brotherhood, kills a man and hides the knife with a young Aryan member sitting behind Wade. In a moment's panic, the young man hides the knife under Wade and forces him to deny knowledge of the knife. As a result, Wade is sent to solitary confinement until the mess can be sorted out. Upon further investigation by Lieutenant Jackson (Harold Perrineau), Jackson is convinced Wade is an accessory to murder, and decides to send Wade to the Security Housing Unit (SHU), of which Jackson is the commanding officer. Life is tough for Wade in the SHU. In addition to 23-hour lockdown days, and the inability to see his family at first, the 1-hour yard days consist of fights, to which the guards bet on. Scared and desperate, Wade initially groups with the Aryans, even going so far as to shave his head. His cell-mate John Smith (Val Kilmer) who was serving a life sentence after avenging the death of his family befriends Wade and gives helpful advice and hope to him.

The story tells the investigation started by symbolist Robert Langdon and a good-looking cryptologist, Sophie Neveu, around the murder of a Museum Louvre's curator. In fact, the unfortunate murdered man was Sophie's grandfather, and the corpse was found with a series of symbols and codes, like a pentagram and a Fibonacci number sequence. But police detective Fache will begin to chase Langdon, who escapes after receiving a warning about the captain's real intentions. Sophie has with her a kind of key with dots and number 24 engraved on it, which opens to her and Langdon a big complex investigation that involves a supposedly heretic theory: Jesus Christ and Mary Magdalene were, in fact, a couple who produced a daughter named Sara. A millenarian sect called The Priory of Sion has kept for centuries the secret of that matter. A masochist and kind of psychopath albino monk, Sibilas, an Opus Dei member, will chase Langdon and Sophie as well, in order to impede that they solve the mystery of Christ and Mary Magdalene, and also the real meaning and location of the Holy Grail. A passionate British researcher, will help Langdon in his quest, revealing to them several symbolisms in Da Vinci's master work The Last Supper, traveling to mythical places in the UK, such as The Church Temple, where it is believed that a group of Templars Knights are buried, and Sir Isaac Newton's tomb at Westminster Abbey, where are located some of the main keys to solve the Holy Grail's mystery.

When Bobby Saint and Mickey Duka meet with European arms dealer Otto Krieg at the Tampa, Florida seaport, the FBI intervenes and Saint is killed while Duka is jailed. "Krieg", supposedly killed in the shootout, is actually undercover FBI agent and former U.S. Army Delta Force operator Frank Castle. Shortly thereafter, he retires from the FBI and attends a family reunion at his father's oceanside home in Aguadilla Bay, Puerto Rico. Tampa crime boss Howard Saint is enraged by the death of his son, and with right-hand man Quentin Glass bribes the FBI for confidential information about "Krieg". Saint orders Castle murdered, and Saint's wife, Livia, demands Castle's entire family be killed as well to "settle the score". At the reunion, gunmen including Glass and John Saint, Bobby's identical twin, kill most of the extended family. Castle and his father kill several of the attackers before Castle's father is killed. Castle's wife and son try to escape in a Jeep, but Saint runs over them with a truck, killing them. Castle, shot in the chest and blown off a pier in an explosion set by Glass, survives and is nursed back to health by a local fisherman, Candelaria. Once recovered, Castle goes to Tampa and takes refuge in an old tenement where three young outcasts — Dave, Bumpo and Joan — live. Castle abducts Duka, who fearfully gives up information about the Saints — whom he, too, hates, and so willingly becomes Castle's mole. Castle starts exacting revenge on the police and FBI agents who have been bribed to close the investigation of his family's murder. In the process, he sabotages Saint's money-laundering business and severs Saint's partnership with Cuban mobsters the Toro Brothers, and starts tailing Livia and Glass, whom he learns is a closeted homosexual. Saint, realizing Castle is alive, sends two assassins to kill him. Castle kills the first, guitar player Harry Heck, by shooting a ballistic knife into Heck's throat. The second is "the Russian", a behemoth who beats Castle in a brutal fight but is defeated when Castle throws boiling oil in his face, blinding him long enough for Castle to throw him down a staircase, breaking his neck. Moments later, Saint's men arrive, led by Glass and John Saint. Dave, Joan and Bumpo hide Frank and refuse to tell Glass where he is, despite Glass sadistically pulling out Dave's multiple facial piercings with a pair of pliers. They leave a man behind to kill Castle upon his return, but Castle kills him once Glass and the others are gone. With assistance from Mickey, Castle manipulates Saint into believing Glass and Livia are having an affair. Saint, unaware Glass is gay, and believing Livia to be capable of cheating on him, kills them both personally, neither of them knowing why. Castle attacks Saint's headquarters, the downtown Tampa nightclub Saints and Sinners, killing many of Saint's henchmen. He kills John Saint by having the crime boss' son hold an eight-pound, trip-wire activated grenade until his arm wearies and the grenade explodes, killing him. Castle wounds Howard Saint with a pistol when Saint attempts to shoot him in the parking lot of the nightclub. Castle then ties Saint to a slow-moving car, but not before revealing that Glass and Livia were not having an affair. Several hidden bombs go off, and the destruction and wreckage culminate in the shape of the Punisher's iconic skull. Later that night, Castle returns to his apartment and prepares to commit suicide, but after a brief vision of his wife, decides to continue his vigilante mission against others who in his mind deserve punishment. Before departing on his next mission, he leaves most of Saint's money for Bumpo, Joan and Dave. On the Sunshine Skyway Bridge, he vows, "Those who do evil to others — the killers, the rapists, psychos, sadists — will come to know me well. Frank Castle is dead. Call me the Punisher."