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.

Frank Castle (Ray Stevenson), who by now has been the Punisher for five years, assaults a party for mob boss Gaitano Cesare. Billy Russoti (Dominic West) escapes to his recycling plant hideout, and Detectives Martin Soap (Dash Mihok) and Saffiotti (Tony Calabretta), who were staking out the party, inform Castle. Castle infiltrates Russoti's hideout, and after a brief firefight, Russoti is thrown into a glass-crushing machine that leaves him hideously disfigured. Russoti later refers to himself as "Jigsaw" because the stitches in his face resemble puzzle pieces. Castle, who takes cover behind the body of Nicky Donatelli (Romano Orzari), discovers that Donatelli was actually an undercover agent. Agent Paul Budiansky (Colin Salmon), the deceased agent's partner, joins the NYPD's "Punisher Task Force", partnering with Soap to help bring Castle to justice. Meanwhile, Jigsaw frees his deranged and cannibalistic brother, "Loony Bin Jim" (Doug Hutchison). Distraught over killing the agent, Castle attempts to make reparations to Donatelli's wife, Angela (Julie Benz), and daughter, Grace (Stephanie Janusauskas), to no avail. Castle threatens to retire from the vigilante business, but his armorer, Microchip (Wayne Knight), forces him to reconsider, telling him Jigsaw will go after Donatelli's family for revenge. Jigsaw, Loony Bin Jim, and two goons, Ink and Pittsy, break into Donatelli's house and hold the family hostage. The Punisher tracks down Maginty (T. J. Storm) a known associate of Jigsaw, executing him after extracting the information before being apprehended by Budiansky and Soap. Castle tells him Jigsaw went after Donatelli's family, and Budiansky sends a police car to check on the Donatelli house, intending to turn the Punisher in. When the patrol car fails to respond, Budiansky checks on the house, where he is captured by Ink and Pittsy. Soap frees the Punisher, who kills Ink and Pittsy before leading Donatelli's wife and daughter away. Budiansky then arrests Jigsaw and Loony Bin Jim after a short gun fight. Jigsaw and his brother bargain with the FBI for their release by giving up Cristu Bulat (David Vadim), who was smuggling in a biological weapon destined for Arab terrorists in Queens, New York. The brothers are granted immunity, plus the US$12 million Bulat was paying to use Jigsaw's port, and a file on Micro. They take Micro hostage, killing his mother in the process. They once again take the Donatellis hostage, after critically injuring Micro's associate Carlos, whom Castle had left to protect them. Castle later arrives at the hideout, and euthanizes Carlos. Jigsaw sets himself up in the Bradstreet Hotel, hiring a small private army of criminals. Castle enlists the help of Budiansky, who informs Cristu's father, Tiberiu Bulat (Aubert Pallascio), where Jigsaw is located. Tiberiu's goons start a shootout in the hotel lobby, affording Castle a distraction. Castle enters through a second-floor window, leading to a firefight with Jigsaw's hired guns. Afterward, Castle engages Loony Bin Jim in hand-to-hand combat; outmatched by his brute speed and agility, but eventually gets his upper hand. Realizing he will probably not survive the brawl, Jim runs away. Castle chases him and confronts both him and Jigsaw, who are holding Micro and Grace Donatelli at gunpoint. Jigsaw gives Castle a choice: If Frank shoots Micro, Jigsaw will let the others go free. Micro bravely offers his life to save the girl, but Castle chooses to shoot Loony Bin Jim instead. As a result, Jigsaw kills Micro. Enraged by the loss of his partner, Castle attacks Jigsaw, eventually impaling him with a metal rod and throwing him onto a fire. As Jigsaw burns to death, Castle calmly tells him, "This is just the beginning." Outside, Angela forgives Castle, who bids farewell to Budiansky and the Donatelli family. As Castle and Soap leave together, Soap tries to convince Castle to give up his vigilante status after having "killed every criminal in town." Soap however changes his mind when he is held up by a murderous mugger who quickly becomes another victim of the Punisher.

In late 19th-century New Mexico, Samuel Jones reappears hoping to reconcile with his adult daughter Maggie Gilkeson. She is unable to forgive him for abandoning the family and leaving her mother to a hard life and early death. This situation changes when Pesh-Chidin and a dozen of his followers (who have left the reservation) pass through the area, ritualistically killing settlers and taking their daughters to be sold into slavery in Mexico. Among those captured is Maggie's eldest daughter, Lilly. Maggie's rancher boyfriend Brake Baldwin was among the settlers killed. The U.S. Cavalry refuses to help retrieve the captive women as its resources are tied up conducting forced relocation of captive Native Americans. This leaves Maggie, her father, and her younger daughter Dot alone in tracking the attackers. The group unexpectedly meets up with Kayitah, a Chiricahua, and an old friend of Jones, who also happens to be tracking the attackers with his son Honesco, because among the captives is a young Chiricahua woman who is engaged to Honesco. After the two agree to join the group, and Maggie treats Honesco's injuries, Kayitah informs Maggie that Jones had been a member of their Chiricahua band where he gained the name Chaa-duu-ba-its-iidan, (“shit for luck”) during his wanderings. It is finally with the combined efforts of the two families that they are able to free the women, at the cost of Kayitah's life, and immediately flee to the mountains with the kidnappers behind them. Knowing they have no other choice but to stand their ground, the group fights off the remaining kidnappers including Two Stone. During the battle, Jones fights El Brujo, the one responsible for kidnapping his granddaughter. When Brujo attempts to kill Maggie with a pistol, Jones sacrifices his life to save his daughter as both he and Brujo fall off a cliff to their deaths. Maggie shoots at the last remaining kidnappers to scare them off. She realizes her father's love for her and finally forgives him.