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 1944, a woman had a boyfriend and was going to get engaged. But her father thought he was poor and tried to use a gun. 63 Years later, moving to a spooky, old house in the country, Roxy Hunter, an irrepressible nine-year old, stumbles into a weird world of unsolved mysteries and the unknown. With the help of her best friend Max, a twelve-year-old genius she calls her fiancé, she embarks on a mission to solve a crime, save their house, and re-unite a lost love from beyond the grave.

Telly Paretta (Julianne Moore) believes that her son, Sam (Christopher Kovaleski), died fourteen months ago in a plane crash, but her husband Jim (Anthony Edwards) tells her that she's delusional and that they have never had a son and even her best friend Eliot (Jessica Hecht) doesn't appear to believe in Sam's existence despite her closeness to him. Dr. Munce (Gary Sinise) tells her that Sam was merely a figment of her imagination and is just imagining a life that might have been. He recommends that she be sent to a hospital, but she runs away and meets with a man named Ash (Dominic West) who she thinks is the father of a girl (Kathryn Faughnan) who was friends with her son and died in the same crash. At first he dismisses her, claiming he never had a daughter, and calls the police. After she is taken into custody, however, he remembers his daughter and rescues Telly. Together they escape and go into hiding, pursued by National Security agents. Telly and Ash capture an agent (Lee Tergesen), whom they threaten. The agent reluctantly reveals that he and other agents are merely helping "them" and that they do so to protect humankind. The roof of the house blows off and the agent, along with the roof, is sucked into the sky — presumably taken by "them"- and Telly and Ash flee. Eventually, Telly visits Dr. Munce again and he reveals that the disappearances are the work of "them," and that the government monitors their trials, all too aware that they have no power to stop "them" from doing whatever they want. Doctor Munce takes Telly to an airport and the dilapidated hangar of Quest Airlines, where he introduces her to an agent of “them” (Linus Roache). He tells the agent that “It’s over,” and to stop the experiment because it will only cause more harm. The agent replies, saying “It’s not over,” and then tells Telly that she has been a part of an experiment to test whether the bonds between mother and child can be diminished. In her case, her memories could not be erased. Telly refuses to deny her son's existence. The agent mentions that if he fails to erase her memory then he will look like a failure. The agent then subdues her and finally succeeds in erasing her memories of her son. During further questioning, though, a question about the name of her son triggers Telly's memory of her pregnancy, and all of her memories of Sam return. This causes the agent to be "abducted" himself, supposedly for his failure to erase her memory. This ends the experiment. Telly finds herself living a normal life, although she remembers everything that has happened. She reunites with Sam at a park. Also at the park is Ash, watching over his daughter. Like Sam, he has no memory of what has happened. Telly reintroduces herself, and the two sit and watch the kids play in the playground.

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."

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.

Two scientists, Dr. Elena Kinder (Diane Keaton) and Dr. Heep (Christopher Lloyd), use genius-baby studies to fund BabyCo's theme park "Joyworld". According Dr. Kinder's Research, babies are supposed to possess vast, universal knowledge and speak a secret yet impossible-to-translate baby prelanguage called "Babytalk". At age two, however, the knowledge and language are lost as the babies "cross over" by learning how to talk. Most of the babies that were raised in Dr. Kinder's vast, underground research facility were adopted from the Pasadena orphanage, transformed into geniuses through use of the Kinder Method, and then used in experiments to decipher the language used by the baby-geniuses. One mischievous toddler, Sylvester (AKA Sly), makes repeated attempts to escape Dr. Kinder's research facility and one night, Sylvester goes into a dirty diaper truck and he actually succeeds. The next morning, one things Sylvester does not expect is to run into his twin, Whit, in a mall playground. Although Sylvester and Whit share a telepathic bond, they have no idea of each other's existence. While the guards from Dr. Kinder's research facility capture Whit, mistake him for Sylvester, and take him back to Dr. Kinder's research facility, Sylvester is taken home by Whit's adopted mother, Robin (Kim Cattrall), who is Dr. Kinder's niece. After Dr. Kinder is horrified that Whit and Sylvester switched at the mall, she decides to do a cross evaluation on Sylvester and Whit. However, when she comes to Dan Bobbin's place, she realizes that Dan Bobbin can understand babies. After the attempts to retrieve Sylvester fail, Dr. Kinder decides to move the research facility to Lichtenstein, so that they can transform Whit into becoming a genius thanks to him getting bred by the Kinder Method (thus erasing his memories about his foster parents, foster brothers and foster sisters) and use him as an experiment to crack the code to "Babytalk". The babies at Bobbin's place hypnotize Lenny (Dom DeLuise), the bus driver to drive to Dr. Kinder's research facility. Once at the research facility, Sylvester goes to the control room to set the robots from the theme park on the lab scientists. When the Bobbins return home, their natural daughter Carrie tells her father that the children are in Dr. Kinder's research facility. At the end of the fight Dr. Kinder captures Whit and takes him to the helicopter pad on the roof. Robin and Dan chase them to the roof, where Dr. Kinder reveals that she and Robin are not related, and that Robin was adopted at age two. After Dr. Kinder got arrested by the police, Sylvester and Whit come together on the roof to cross over. Dan and Robin adopt Sylvester. Dan is still curious of the secrets of life, but as the twins have crossed over they no longer know those secrets. Carrie, their sister, doesn't reveal anything (just gives her dad a sly smile) because adults aren't meant to know their secrets.

Young Cuban Rafael just buried his mother, and comes to Houston to meet his father John for the first time. The difficult part is that John doesn't know he is Rafael's father. John runs a dance studio, and everyone prepares for the World Open Dance championship in Las Vegas. It soon becomes clear Rafael is a very good dancer, and Ruby is the biggest hope for the studio at the championship.

Jerry Maguire (Tom Cruise) is a glossy 35-year-old sports agent working for Sports Management International (SMI). He writes a mission statement about perceived dishonesty in the sports management business, "The Things We Think and Do Not Say: The Future of Our Business." Management sends Bob Sugar (Jay Mohr), Jerry's protégé, to fire him. Jerry and Sugar call all of Jerry's clients to try convincing them not to hire the services of the other. Sugar secures most of Jerry's previous clients. Jerry speaks to Arizona Cardinals wide receiver Rod Tidwell (Cuba Gooding, Jr.), one of his clients who is disgruntled with his contract. Rod tests Jerry's resolve through a very long telephone conversation, culminating in the famed "Show me the money!" scene. Meanwhile, . Frank "Cush" Cushman (Jerry O'Connell), a superstar quarterback prospect from Southern Methodist University expected to be number one in the NFL Draft, also stays with Jerry after he makes a visit to the Cushman home. Leaving the office, Jerry announces that he will start his own agency and asks if anyone is willing to join him, to which only 26-year-old single mother Dorothy Boyd (Renée Zellweger) agrees. Jerry is dropped by Cushman and breaks up with his disgruntled fiancée. He then turns to Dorothy, becoming closer to her young son, Ray (Jonathan Lipnicki), and eventually starts a relationship with her. However, Dorothy contemplates moving to San Diego as she has a secure job offer there. Jerry concentrates all his efforts on Rod, now his only client, who turns out to be very difficult to satisfy. Over the next several months, the two direct harsh criticism towards each other with Rod claiming that Jerry is not trying hard enough to get him a contract while Jerry claims that Rod is not proving himself worthy of the money for which he asks. Jerry marries Dorothy to help them both stay afloat financially and to keep her from moving away. He is emotionally and physically distant during the marriage but is clearly invested in becoming a father to Ray. Although Dorothy loves Jerry, she breaks up with him because she believes that he does not love her. Before the start of a Monday Night Football game between the Cardinals and the Dallas Cowboys, Sugar tries stealing Rod, but Rod and Jerry rebuke him. The two reconcile soon after. Rod plays well but appears to receive a serious injury when catching a touchdown. He recovers, however, and dances for the wildly cheering crowd. Afterwards, Jerry and Rod embrace in front of other athletes and sports agents and show how their relationship has progressed from a strictly business one to a close personal one, which was one of the points Jerry made in his mission statement. Jerry then flies back home to meet Dorothy. He walks in and, in front of her friends, says "Hello." He then speaks for several minutes, telling her that he loves her and wants her in his life, ending with the statement, "You complete me." Dorothy's reply to Jerry is, "You had me at 'hello.'" Rod later appears on Roy Firestone's sports show. Unbeknownst to him, Jerry has secured him an $11.2 million contract with the Cardinals allowing him to finish his pro football career in Arizona. The visibly emotional Rod proceeds to thank everyone and extends warm gratitude to Jerry. Jerry speaks with several other pro athletes, some of whom have read his earlier mission statement and respect his work with Rod. The film ends with Jerry, Dorothy, and Ray walking in the park and stumbling across a Little League Baseball game. When the ball lands near them, Ray throws it back. A surprised Jerry then comments on his natural throwing ability (and possible future in sports), much to Dorothy's dismay.

Lee Reyes plays Hiro, Master Tetsu's (Pat Morita)'s grandnephew, who is the last of the true ninja. His granduncle sends him to apprentice under Joe Kastle, (David Bradley), who is the American Ninja, to gain experience. Hiro cares only for his Game Gear and has little interest in the ways of the ninja. Joe in addition to being the American Ninja also owns a boat. In order to meet the American Ninja, Lisa (Anne Dupont) "varnishes" his boat when in fact she was asked to "tarnish" it. While having dinner Lisa is kidnapped by Viper (James Lew) and a host of multi-colored ninjas, and so the American Ninja and Hiro sneak onto a plane to Venezuela to save her. It is revealed that Lisa is the daughter of a scientist, under the employ of Glock (Clement von Franckenstein), who is being forced to develop a nerve gas for a Latin American despot. Ninja fighting ensues. Before the American Ninja and Hiro can rescue Lisa and her father from "Viper", the mysterious ninja that appears and reappears with a puff of smoke, the American Ninja must reawaken the ancient ninja tradition within Hiro with a 5 minute training montage. Viper is defeated in a climactic airplane battle scene, and Joe returns to Los Angeles to kiss Lisa on the bow of his boat.