Twelve-year-old Ann Uekusa and her mother move to the small town of Shimane, where Ann's grandparents live and everyone seems to be familiar with everyone else. Ann soon becomes friends with Daigo, a young boy who lives in Shimane, as well as Fuji and Shika, Fuji's younger sister and her best friend in Shimane. When Ann's mother, Miwako, commits suicide, Daigo helps Ann cope with the sudden change in her life. They fall in love, but Ann's life can only become more complicated when her estranged father suddenly arrives from Tokyo. After greatly contemplating going to Tokyo to live with her father after he asks her, she decides to stay. Ann tells Daigo about her decision but makes her go anyway. Ann and Fuji both live in Tokyo but hardly ever talk because Fuji goes to an elite high school, K High. Ann met back up with her friends she had before moving to Shimane and they continue their friendships. In Tokyo, she ends up becoming closer to Fuji, which causes conflict between her and Daigo.In Shimane, Shika learns the truth about her parentage and in her confusion, she begins to fall in love with Daigo. When Ann returns to Shimane, Shika upsets Ann's fragile emotional state so that Ann and Daigo will break up. In the end, Ann breaks up with Daigo for fear that her own sadness will weigh him down. Ann returns to Tokyo and starts a relationship with Fuji; however, because she does not love him, the relationship does not last. Daigo refuses Shika and rumors begin to circulate that he is interested in his middle school classmate Ayumu, who has been helping him studying to get into university and become a teacher.Nearing graduation, Ann learns that her father and his friend Kaede Kuroki have been dating and she is pregnant with Ann's half-sister. Ann's father and Kaede marry after being encouraged by Ann and Ann's grandmother. Fuji, now aware that Shika was the child of his mother's affair rather than himself, supports her decision to studying abroad in Vancouver so that she can learn not to rely on others. Daigo and Ann make it to the post-secondary institutions of their choice while Fuji must repeat his senior year after running away from home.After attending her middle school reunion, Ann spends some time with Daigo, where he tells her to find her own happiness. Six years later, Ann meets a young businessman named Keiichiro Sakura and they become engaged shortly after. After Ann learns that he only uses people for his own gain, she confronts him about his insensitivity, but he is disappointed in her and breaks off the engagement. Almost a week afterward, she takes a train to Okayama, where Daigo teaches elementary school. Ann's grandmother, meanwhile, believes Ann will suffer the same fate as her mother. After a failed suicide attempt on the beach, Ann is taken to the hospital and later meets Daigo, who asks her to marry him. She says yes and at the very end the two are shown to be happily married with an infant son named Ryo. Meanwhile, Fuji decides to marry his cousin Mariko (against his family's wishes) and Shiika decides to work for her uncle in America.

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.