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- When Donald Lucas, the imprisoned Jack-of-All Trades killer, manages to hack onto the Internet, Bailey fears that he is communicating with a disciple. The investigation leads the VCTF to a small and very strange northern California town, named Otis, which is plagued by a series of Jack-of-All-Trade murders. With the assistance of the crackpot Sheriff Ed Post, Sam, Bailey and the team try to find the suspect. But George gets abducted by the suspect, whom is connected to a reclusive, wheelchair-bound professor, named Philip Menzies, who is later murdered. The search leads to an underground lab where Sam discovers her father once worked there for his government-sponsored mind-control experiments that Lucas was one of the test subjects involved in.
- When the twisted, serial killer, Jack-of-All-Trades, murders a kindly neighborhood fix-it man, Sam discovers a pattern: her unseen tormentor is leaving messages to her through his victims, all of whom had some connection to her. As Sam agonizes over her slain acquaintances, her new beau Cooper and Bailey try to comfort and protect her. But they can't watch her all the time: unlike Jack who sets out to antagonize her more when he targets Cooper.
- Sam, Bailey, Grace and the VCTF are called in to investigate a serial rapist terrorizing the Florida panhandle. The victims are able to provide the team with a number of clues which Sam uses to form her profile of the assailant. In the midst of the investigation, Sam butts heads with a local female sheriff, Anita Pessoa, who continuously criticizes the VCTF's handling of the case. Sam confronts Pessoa and eventually learns the woman was once a rape victim herself. Back in Atlanta, John and Marcus get a hot tip on the fugitive Sharon Lesher. Desperate for cash, she has made it known on the street that she is looking for Jimmy Coniglio, one of her old partners in crime whom betrayed her in which she was sent to prison four years ago for an armed robbery that Jimmy actually committed. John and Marcus plan to use Jimmy to capture Sharon in a sting operation.
- This crossover episode picks up after the ending of End Game (1999).Bryce, a brainwashed child prodigy, leaves home to join "The Father" who uses him to begin his revenge. Jarod from End Game (1999) joins Sam and Bailey on the case.
- When a series of murder victims are found arranged in elaborately staged tableaux, Sam, Bailey and the team deduces that the killer is replicating famous artworks with their lifeless forms. Her investigation plunges her into the avant-guard art world until she accidentally strays into the killer's lair, where he takes her hostage and prepares to use her for his latest three-dimensional "masterpiece." Meanwhile, the unseen, clever serial killer Jack of All Trades has compromised the team's vital computer system by hacking in and planting various viruses to offset Sam even more. Also, Sam tries to spend more quality time with Chloe when work takes her away.
- When Jack of All Trades, the inventive but frighteningly elusive serial killer stalking Sam, continues to toy with members of the VCTF team and their families, Bailey orders everyone into the task force's bunker-like command center (Angel and Chloe, Grace's husband, George's gay lover, and Brubaker's brother) as they scramble to devise a trap to ensnare Jack. Since their technologically brilliant quarry delights on eavesdropping and seeing them almost everywhere, the frustrated team uses Sam and Grant as bait to try to flush Jack out into the open. Unsuccessful on two times, they trace a hit man hired by Jack to his lair which is a children's Catholic orphanage where Jack again escapes, but is forced to leave his lair and processes behind.
- In the two-part season final, the team tries to catch a diabolical killer determined to take revenge on people who are so blinded by their love of money that they can't see the repercussions their actions have on the other side of the world, starting the with the setting off of incendiary car bombs outside a wealthy business office. The game between Jack and VCTF begins with Sharon as bait to lure Jack to the prison so they can catch him. Meanwhile, Sam pays a visit to her long estranged father for the first time in 10 years. As she struggles to both deal with her father, and the elusive avenging killer still committing bombings across the country, she soon makes the final connection to the killer in order to catch him. Also, Bailey goes to extremes for Frances's future when she's accepted into a prestigious college in Boston, but is forbidden to leave Atlanta as a condition of her parole.
- The separate kidnappings of two high-profile doctors and the evidence left behind leads Sam to believe that the prime suspect is a patient with an incurable medical condition who is driven to take desperate measures. Meanwhile, Bailey is riddled with guilt when he develops a mutual attraction with the wife of one the missing men. Also, the unseen Jack-of-All-Trades continues his quest to isolate Sam by targeting Agent Brubaker and terrorizes him by dropping his jalopy on him while he's fixing it.
- In another cross-over from the series 'Pretender' of episode 'Spin Doctor', Rachel and the VCTF work with Jarod when two dirty Secret Service agents, who are their most direct link to the killers of a fellow agent, are found slain. However, while romantic sparks fly between the pair, Jarod suddenly disappears and is tortured by the murderer Todd Baxter, who is on a crazed mission to eliminate everyone he thinks is involved in the agency's corruption. Meanwhile, Grace learns of George's addition to painkillers and pep pills and threatens him to quit or she'll inform on him.
- Sam, Bailey and John must find a twisted assassin before he kills a celebrated political candidate. The clues lead them to a famous pop singer, named Morrisa, whom is also targeted by the stalker. But Sam is distracted by new evidence that could locate her own murderous stalker, "Jack-of-All-Trades." Relying on audio clues from a recording that he leaves, the hopeful FBI agents zero in on a Baltimore church which they believe to be Jack's lair, only to find the place cleaned out and a message from Jack saying he will be coming after Sam.
- Dr. Samantha "Sam" Waters is a brilliant female forensic psychologist with a unique gift for understanding the criminal mind and a special skill that enables her to "think" in pictures and visualize a crime through the eyes of both the victim and the killer. Three years earlier, an admiring serial killer called "Jack of All Trades" murdered her husband, leaving her devastated. Guilt-ridden, Sam had retired and retreated with her seven-year-old daughter, Chloe, to live an anonymous life with her friend, Angel Brown, in rural Maryland. Sam is coaxed out of her self-imposed isolation by her old friend Bailey Malone, head of the FBI Investigative Support Unit, to assist in solving a baffling spate of weekend serial killings that have claimed the lives of several single women in Atlanta, but she is unwilling to make her presence known since she still lives in fear of Jack, who is still after her.
- Sam figures out the identity of the so-called 'venom killer' as Robin Poole when a victim, suffering from sea wasp jellyfish stings, disappears from the hospital and it was Robin impersonating a victim. John and Cooper travel to Arkansas to investigate Robin's origins for her murderous lifestyle. Bailey takes drastic measures to curb the carousing Frances by deciding to send to a reform school, in which she shoots him with his own gun. John debates the future of his intimate relationship with Angel and they both agree to split up. After a few taunts, Jack strikes again, first by framing the FBI and VCTF by impersonating an agent and beating up a few suspects, and then abducts both Sam and the 'venom killer' Robin Poole, and taunts the VCTF by filming it on an Internet web site.
- Sam interrogates inmate Arthur de Rhodes, a serial killer whom she put in a prison for the criminally insane six years earlier, over a recent murder of an elderly man from poison gas inhalation that bears striking similarities to his modus operandi. However, when another murder occurs, Sam wonders whether the culprit could possibly be the clever de Rhodes, or a copycat killer. All bets are off when de Rhodes eventually escapes, and no one is safe, especially Sam. Meanwhile, the unseen Jack of All Trades now begins to target and terrorize Angel to drive her away from Sam.
- Sam and the task force probe a series of ghastly murders which are carefully videotaped and sent to TV newsrooms by a vigilante who announces that the crimes are righteous retribution against guilty people who slip through the judicial system. When a young Brooklyn woman is kidnapped and thought to be alive, Sam, Bailey and John accelerate the investigation to former law students with strong opinions about crime and punishment. Meanwhile, Grace secretly takes a leave when she realizes that she's pregnant. Also, the unseen Jack of All Trades is revealed to be alive and settled in another lair while continuing to spy on Sam and taping her phone line.
- Sam Waters joins the newly formed Violent Crimes Task Force (VCTF), based in Atlanta and led by her mentor, Bailey Malone, and assisted by detectives John Grant and Nathan Brubaker, forensic specialist Grace Alvarez, and computer hacker George Fraley, to probe a string of well-publicized arson fires in the Deep South, until her anonymity is shattered by her murderous, unseen stalker, Jack-of-All-Trades. As a result, Sam is forced to move with her daughter Chloe and her best friend, Angel, away from their country house, while she uses her skills to compose a profile of the self-destructive arsonist before he strikes again.
- When a hospital is the target of a bombing attack, the VCTF is called in to investigate. They are dealing with a highly skilled explosives expert who obviously has an agenda in mind. Bailey summons Cooper to Atlanta to assist with the case. His return is awkward for he and Sam as they have previously ended their romantic relationship. With Frances finally in custody, Bailey must deal with her legal problems as the prosecutor sees her case as a stepping stone for political office and is determined to see her do jail time for shooting her father and fleeing prosecution. Meanwhile, George also faces difficulties as he continues to be pressured by an old acquaintance to embezzle funds from a local bank. This "pressure" becomes threats of violence when the guy's muscle, the mysterious Marcus Peyton, whom turns out to be an undercover policeman. Coop manages to capture the bomber, only to be abducted by Jack and killed by his lethal companion, Jill, whom are impersonating ambulance workers.
- When Native American chiefs are ritually murdered on an Arkansas reservation, Sam, Bailey and Grant tiptoe around local suspicions and superstitions as the locals blame a 1,000-year-old spirit, the Nacazanti, and a perplexed Sam consults a tribal wise man to narrow the list of suspects. Back in Atlanta, the unseen Jack-of-All-Trades steals Bailey's FBI identification card and uses it to entrap and kill a woman, and frame Bailey for the murder.
- Sam and the team investigate a series of bizarre killings whose victims were connected to the trial of a charming murderer on death row sentenced to die within days. One of her prime suspects is a love struck protester who leads a candlelight watch outside the prison while appeals are filed to halt the execution. Elsewhere, the unseen serial killer and master of disguises, Jack-of-All-Trades, assembles a roulette wheel with pictures of the entire VCTF unit: and one spin will determine his next victim.
- Still investigating the reunion killer, Sam determines that one of her friends, Greg or Monica, is the likely killer. With the VCTF hot on his trail, a wounded Jack escapes to his lair to recuperate from being shot. In attempting to pursue Jack, as well as the killer of her friends, Sam begins to wonder if it's all becoming a bit too overwhelming. Meanwhile, Frances attempts to give herself a 18th birthday 'present' by seducing John. The plan fails and John calls Sam to help him take the ever rebellious teen home to her father. Bailey asks Marcus Peyton to join the VCTF team and he accepts, to John's dismay. The team finally corners Jack at a convalescent home where he has gone to get painkilling drugs for his gunshot wound. But Jack hides in a body bag of one of the deceased residents and makes another clever escape.
- Sam and the VCTF team investigate a series of bizarre murders where the victims are either crushed or strangled with silver coins. As the killings become more violent, Sam puts the evidence together to conclude that the killers are linked to a recluse millionaire named Charles Vanderhorn who may know the identity to the killers. Meanwhile, Sam and the rest of the team get a lead on the elusive Jack of All Trades when a man named Austin Keller whom has the suspicious nature of Jack is identified, but he flees by plane to Costa Rica.
- A series of bomb blasts at power plants draw Sam, Bailey and the rest of the task force to Pittsburgh, where Sam meets a charming ATF bomb squad dismantler, named Nick Cooper, and the flirtatious pair quickly form a romantic bond. Even so, their primary focus remains on targeting a deranged man, with an obsessive fetish for cleanliness, who targets Grace as his liaison between the authorities, while he is working on a masterwork blast to poison the city's water supply in just hours.
- Sam, Bailey, Grace, and Nathan are taunted by a diabolical female serial killer who prefers to use a variety of exotic poisonous animals, (tree frogs, spiders, snakes, etc.) to kill her victims, while providing her pursuers with cryptic clues to her next murder. Meanwhile, John, now back working for the Atlanta police, arrests Francis during a drug raid and tries to talk some sense into her. A frustrated Bailey is further irritated by the arrival of a sexy private investigator, named Christine Logan, who tries to aid the VCTF, but it's the unit's chief nemesis, a jealous Jack of All Trades, who ironically can help the most when he sends fax messages to Sam of clues to the killer's identity. Also, Bailey asks Cooper to replace John on the team while Brubaker decides on a transfer.
- A series of vigilante ax murders of abusive husbands leads the Sam, Bailey and the rest of the VCTF team to an eccentric and reclusive cartoonist, named Evie Long, whose work has apparently influenced the killer. Meanwhile, Sam finally confronts the imprisoned Sharon Lesher (Jill of All Trades) and tries to solicit her help in finding and identifying Jack. But Sharon is very hostile and refuses to cooperate, knowing Jack will eventually try to break her out of the prison, while Sam tries to convince Sharon that Jack intents to kill her to prevent her from talking. Also, Sam becomes nervous when she plans to receive an award from the American Association of Women in Law Enforcement.
- As Bailey clings to life in an Atlanta hospital following the shooting, Sam and the team are forced to take on a high profile case involving an international serial killer. The murderer, named Ashok Dupree, has escaped from an prison in Calcutta, India and comes to the U.S. for the purpose of killing a celebrity, so that he too can become world renown. While working to bring the killer to justice, Sam must convince herself and the overzealous FBI director Lou Handleman, that she is innocent of the murder that Jack actually committed. Also, John decides to return to the VCTF, and Bailey's daughter, Frances, now on the run as a fugitive, contacts John to check on her father's condition.
- The task force comes under intense scrutiny when the FBI suspects that an insider is selling covert information. Bailey agrees to a mock field training exercise designed to root out the mole, where he learns that one of the agents, Art Behar, has a personal grudge against him for being involved with Behar's ex-wife, Ellen. When one senior investigator, Ed Portero, is found murdered in the command center, Sam tries to profile which one of the team's edgy members might benefit the most from trading FBI secrets. Meanwhile, Grace goes public with the news that she's pregnant, and Nathan stands at the crossroads of the future of his bumpy marriage with his lawyer wife Michelle.
- The VCTF is summoned to New Orleans when the murder of a research librarian has the markings of a Jack kill. Sam is perplexed by what appears to be inconsistencies with Jack's prior modus operandi. It turns out that Jack-of-All-Trades is wreaking havoc with his new lethal partner-in-crime, Sharon Lesher, whom becomes Jill-of-All-Trades. Meanwhile, Bailey meets his new boss, Art Behar, whom threatens to shut down the VCTF since he still holds a grudge against Bailey for dating his ex-wife. Also, George is confronted by his past misdeeds when a corrupt attorney asks him to use his computer hacking skills to embezzle funds from a local bank.
- In the two-part season final, the Donald Lucas trial begins as the team heads out to Mexico where in the small town of Las Brisas, women have been vanishing without a trace for the past year, and some corpses have been discovered. But their investigation is hampered on both sides of the border by the corrupt police chief, Miguel Villalobos, whom is under the thumb of a U.S sheriff, J.D. Tollman, whom try to derail the VCTF's investigation when the murders lead to a powerful U.S. businessman, named James Lofton, running a textile factory in Las Brisas and has been in the company of local prostitutes, some of whom ended up as victims. While assisting Marta Fernandez, a loyal policewoman with the investigation, Sam and the group commute back and forth to Atlanta for Lucas' trial with testimony from her, Bailey, George, against Lucas. Also testifying on Sam's behalf is Sheriff Ed Post from Otis, California who, unknown to everyone, is actually the real Jack-of-All-Trades whom has been in hiding all this time and is using Lucas, his disciple, to get close to Sam.
- Sam, Bailey, Grant and Brubaker race the clock to track a serial kidnapper who curiously abducts a wide range of women from a college co-ed to a senior citizen. Based on his ritualistic clues, Sam deduces that they have only hours before the victims are executed. While in pursuit, agent John Grant is wounded during a shootout with the abductor, and the trail cools off until Sam gets an unlikely break when she finds a stripper who survived an attempted kidnapping. Meanwhile, Sam's daughter, Chloe, continues to have recurring nightmares about being accosted by a mysterious man, whom Sam discovers that she witnessed Jack of All Trades killing her husband that day.
- One of Sam's first profiles resulted in a man being sentenced to death. Ten years later when the man is about to be executed, murders begin happening that match the m.o. of the prior killings. Ballistics evidence proves the same gun was used for all the crimes. Sam, feeling culpable for what might have been a deadly mistake, reopens the investigation. Evidence leads to a lowly bicycle courier who is mortally wounded when he resists arrest. Once the dying man is in custody, the death row inmate is released from prison. Though a wrong seem to have been righted, Sam still feels something is amiss.
- A burned-out Sam takes somber note of a psychic-turned-author, Elliott Wykoff, whose cooperation with police in solving serial murders has taken a heavy toll on his emotional stability. But worst of all, he's targeted by a serial killer intent on putting him out of his misery. Meanwhile, John chafes under Bailey's strict policy and hard-nosed code of secrecy. When John gets an offer to re-join the Atlanta police, he accepts. Also, Bailey has more problems at home when he attempts to rein in the trouble-prone Francis.
- The VCTF is called in to investigate the seemingly random murders of four people beaten to death during a rainstorm. Sam and the team consults with a psychologist who informs them of a syndrome where people become extremely violent in response to certain types of weather. The clues lead to a construction worker afflicted with the seasonal disorder. Meanwhile, Sharon Lesher, a young felon is released from prison and is met by her pen pal, Jack, whom he takes back to his lair and it becomes clear this is the beginning of an "unholy alliance." Also, Bailey laments the fact that the police plan to charge Frances with attempted murder once they determine her whereabouts.
- The day after getting shot by the real Jack-of-All-Trades, a wounded Bailey calls upon FBI profiler Rachel Burke to find Sam after Jack kidnaps her and subjects her to tortuous mind games by confining her within an abandoned warehouse and trying to get her to be like him in killing to achieve a sense of superiority. In the meantime, Rachel quickly weeds out the self-serving confessions of Donald Lucas whom she correctly assumes was a pawn in Jack's game and by questioning Samantha's father about her history, finally learns Jack's real identity as Albert Newquay and of his methods.
- A kidnapped Sam stalls for time as the murderous Jack of All Trades twists the facts hoping to convince her that she too will kill, when the subject and timing are right. Meanwhile, a recovering Bailey and the new profiler Rachel Burke grope for clues about Jack's hideout. But Jack shows a new card when he lures Chloe into his web of deceit by convincing her that her mother was responsible for her father's death.
- Ohio's cities are being terrorized by a seemingly random sniper. On the scene, Sam, Bailey and the rest of the team are perplexed by the sniper's ability to shoot from increasingly long distances. This ability reminds Bailey of an elite task force he encountered while serving in Vietnam. Bailey obtains from Casper, his secret intelligence source, the names of the task force members. Sam uses clues left at the crime scenes to put together a profile that suggests the sniper is trying to create his own mythology, much like the Archer in Greek literature. Meanwhile, John and Bailey look into Lou Handleman who has tried to discredit John by using Frances. But when they attempt to arrest him, Handleman resists and accidentally shoots himself. Also, Jack travels to Aurora, Illinois to find the runaway Sharon in her home town to bring her back, or kill her.
- Sam investigates a series of murders which bear striking similarities to the methods of a killer whom Bailey put in prison 10 years earlier. Sam suspects that the real culprit is still free, and through her gifted insight, she finds clues in the ancient I Ching art of divination that lead her to a high-ranking military officer who may be protecting the killer.
- In Costa Rica, Samantha and the VCTF team finally capture Austin Keller whom they suspect is Jack. Upon arrival back in Atlanta, Samantha continues to investigate the Vanderhorn murders as well as seeking solace with Coop over the recent events. But Samantha is not sure if Austin Keller is Jack of All Trades, or an insane wannabe. Samantha then finds herself as a mediator in a hostage situation when the last surviving killer of the quartet of Vanderhorn killers is holed up in a TV station with Charles Vanderhorn as his hostage.
- A killer's belief he was switched at birth leads him to kill those he feels stole his identity. Two men, born at the same time and in the same hospital as the killer, are brutally murdered. Sam and the team is called in once the link between the two victims is established. Evidence leads the team to an insane woman who believes her baby was switched at birth. The woman swears the badly deformed baby she was given in the hospital, was actually the child of someone else. She was never able to prove that charge, and unfortunately for the baby given to her, she was a cruel and abusive parent. Meanwhile, Jack reverts back to his old murderous form when he kills his mother's butler when he learns the man has been following him at his mother's behest. Also, Sam is concerned about Chloe when she feigns being sick in order to miss school. The problem is revealed to be that Chloe has to write an essay on her parent's occupation and she's afraid to talk about her mom's secret job.
- Bill Porter, a desperate father, kidnaps Sam's roommate, Angel, in a last ditch effort to save his son from the electric chair. Porter's son, Scott, has recently been convicted of murder committed during a robbery. The father believes his son to be an innocent bystander and wants Sam and the VCTF to prove it by interrogating the two suspects whom were suspected in the robbery. Also, Jack plots to break Sharon out of prison first by tapping into the prison's blueprints to know the building.
- Sam and the VCTF are invited to an on-going investigation on the murder of a teen beauty whom was killed a year ago, and no arrests have been made. Bailey and the team first think the parents of the first victim did it. But they find a killer on death row with matching breaking and entering technique, but Sam thinks the convict didn't kill his victims. Meanwhile, Bailey's budding romance with Ellen Behar makes his ever resentful daughter, Frances, more than a little jealous. Sam tries to give more confidence in Chloe who resents her school friends being better looking than she. Also, the still unseen Jack of All Trades escalates his harassment of Sam by mailing her a ghoulish board game detailing his next move.
- The youngest member of an orphaned clan kills to keep his dysfunctional family together. The first murder occurs when the young man kills the boyfriend his sister is considering marrying. Her marriage would result in her leaving the family and that would be unacceptable. Sam profiles that the killer is someone who has felt loss and who is desperately trying to hold on to something he values. The VCTF eventually discover this decidedly unconventional family and at first, mistakenly believe the physically abusive eldest brother is the killer. Sam soon realizes, however, that there is another, more emotionally immature force at work. Meanwhile, Bailey realizes his ex-wife, Janet, is seriously involved and considering remarriage. Also, Chloe is upset when Sam invites her new boyfriend, Paul, over for Christmas.
- Sam and the VCTF investigate the "prime time kidnapper," a madman who has a pathological need for media attention and projects his mania onto an attractive but terrified local TV anchorwoman, Nikki Ware, whom he wants to exclusively cover the prisoner exchanges. Meanwhile, Sam worries about what's really behind her daughter Chloe's reluctance to perform in the children's ballet. Also, the murderous Jack-of-All-Trades makes plans for the release of his imprisoned Jill/Sharon, by killing a prison guard and planing to impersonate him.
- When a North Carolina murder occurs that bears all the markings of an unsolved serial case from 1957, Sam and the VCTF team investigate and discover a fingerprint not previously detected. This enables the team to I.D. the killer, who turns out to have committed suicide prior to the most recent murder. Sam talks to a writer who researched the original case and learns of a young boy who claimed to have witnessed one of the crimes. Meanwhile, Jack (whose real name is finally revealed as Albert Newquay) recuperates from his gunshot wound at the home of his wealthy, but equally deranged mother, Miriam in Maryland. With Jack gone, Sharon redecorates his lair by eliminating all traces of Sam. Also, Sam's in-laws come to town to see Chloe perform in a school play and are angered when Sam is unable to attend. Her absence results from the pregnant Grace going in to labor while the team investigates a crime.
- The VCTF team is on the trail of a serial killer in Chicago who seems to be taking aim at people he deems corrupt. Jim Henegar, the Chicago detective investigating the murders, is reluctant to relinquish control of the case, and he becomes a hindrance to Sam and the team. The evidence leads to a judge, MacGruder, whose son was corrupted in one way or another by the three victims. At the same time, Bailey, who is still healing from the shotgun wound inflicted by his daughter, receives an unexpected phone call from Francis who is still on the run and whom he tries to persuade her to return home, but to no avail. Also, the still unseen Jack angrily rips down his wanted sketch posters from post offices and sends the VCTF a package that includes his own artistic self portrait made from the hair and teeth of his past victims.
- In the cliff-hanging series final, Rachel is emotionally distraught after Danny's sudden death from a drug overdose and she's further rattled by the continuing mind games played by the wanted ex-Agent Marks, whom she believes is responsible for her brother's death as well as a sudden a series of murders which several men are found electrocuted by an unknown device. But Marks does not plan to kill Rachel, for he needs her to accomplish his own agenda with catching a certain Damian Kartais, an unknown serial killer and master of disguises whom has recruited Marks for these killings. Meanwhile, Bailey has even more concerns when he is ordered to conduct a senatorial performance review of his VCTF members as rumors fly that the elite unit will be disbanded.
- Sam and the VCTF investigate a series of fatal hit-and-run auto accidents on remote highways where the only clues are abandoned car hulks, a pattern which leads Sam to suspect a trucker who is reliving a traumatic accident from his childhood. Meanwhile, George is mugged and nearly killed in a video store holdup. Elsewhere, Bailey feels responsible for not being around when Francis begins cutting school and hanging out with a rough crowd. Also, Angel is very appreciative when John speaks to her art class and a romance develops between them.
- The team investigates a serial rapist-turned-murderer in Illinois, whose sporadic timing of the attacks puzzles Sam as well as the connection between his victims whom are left in the woods. Sam figures out that the killer is an angry and frustrated married man taking out his rage and frustration on about-to-be-wed women. Meanwhile, with Donald Lucas, the Jack-of-All-Trades killer finally captured and imprisoned, Sam searches for a new house for her and Chloe.
- Two men are killed, and in both instances, their organs are delivered to hospitals minutes before they are needed for transplant surgery. Sam and the team profile the murders and determine their suspect is someone who was probably an organ recipient in the past. Now, he is returning the favor by providing organs for people with his same rare blood type. Meanwhile, Art Behar, Bailey's boss, sets him up to take a fall in a witness tampering scandal. But John, Marcus and George find evidence that clears Bailey and nails Behar once and for all. Elsewhere, Jack becomes displeased when he learns Sharon has struck up a friendship with the friendly proprietor of a local news stand. Jack kills the man, and angrily asserts Sharon that "he" is her one and only friend. Also, Chloe is followed by a man whom is revealed to be a private investigator hired by Sam's in-laws.
- Someone is killing the young and beautiful in Florida's trendy South Beach by decapitating the victims and leaving their heads on public display. Sam profiles that the killer is striking against beautiful people as a result of his low self-esteem. Evidence eventually points to a young shipping magnate, named Thomas King, who has squandered his multi-million dollar inheritance on South Beach's cosmopolitan lifestyle. Instead of blaming himself, he is now striking out at those who helped him spend his fortune. Meanwhile, Grace attempts to reconcile the strained relationship she has with her Cuban-American mother. Also, the detective on the case, Mario Monagno, falls for Sam and tries everything he can to land a date with her.
- When a talented concert pianist is found slain, Rachel suspects the victim's prodding parents until she discovers the young woman was pregnant and that her baby was forcibly delivered and kidnapped. But her biggest surprise comes when 'Pretender' Jarod returns. While the two indulge their mutual romantic passion, Jarod's mission is to help Rachel deal with the threat posed by Marks, the fugitive FBI agent who delights in stalking and tormenting her. Jarod finds out that Kim Doyle is the one leaking classified information to Marks, but she is killed by the renegade Marks before the VCTF can arrest her.
- After a police officer and other authority figures are found stabbed in their backs, Rachel centers her investigation on a young woman, Pamela Martin, a serial killer who is reported to have assumed multiple identities which probably spring from memories of early child abuse. But Rachel faces an even greater personal threat from FBI honcho Joel Marks who has falsely accused her of forcing a sexual relationship of a subordinate, John Grant, a charge that could ruin her career. Meanwhile, Rachel heats up her romantic relationship with Tom Arquette. Also, Bailey confronts George over his reliance on prescription drugs and orders him to get help.
- Ritualized murders are occurring in Atlanta and in neighboring states. The victims are stabbed and their homes are vandalized with gang-like graffiti. The VCTF is called in and focuses on the son of two of the victims. Further investigation reveals that the son is under the influence of a "Heaven's Gate"-like cult. Sam goes undercover to infiltrate the cult. Meanwhile, Frances continues to cause discord between John and Bailey by claiming that John seduced her. Sam's former mother-in-law continues to object to her raising Chloe and resorts to legal matters to gain permanent guardianship of her. Also, Jack sends Jill out to kill Sam's former mother and father-in-law. But she backs out at the last second and flees Jack's custody which proves damaging when Sam and the VCTF finally learns Jill's true identity.
- The dead bodies of badly beaten men are being found in the Boston metropolitan area. Sam and the team quickly surmise these men were involved in some sort of deadly, ultimate, bare-knuckle fighting match. Searching local hospitals, they find a participant in one of the fights. Sam is able to put together from talking to him and researching the backgrounds of the victims, that all were desperate men in need of money. All the men have a bookie in common and the team eventually gets this man to confess his role in the murders. To catch the fight's mastermind in the act, John goes undercover as one of the fighters.
- Martin Zahn, a zealous anti-nuclear scientist leading a cadre of steely commandos, capture a banquet room full of Washington D.C. brass, and vow to kill them unless the President agrees to meet their demands to ban nuclear weapons. Sam tries to negotiate when they take her hostage as well. While Bailey, Cooper and John debate what to do, Zahn and a few surviving terrorists escape and are cornered in an airplane hanger, where a desperate Sam tries to "profile" the anguished scientist, hoping to find a common bond that might save both their lives. In the meantime, Bailey learns that his estranged, 17-year-old daughter, Francis, has ran away from the home of his ex-wife in Baltimore and lands in jail for robbery. Also, a nun of the orphanage that Jack of All Trades formerly resided at, recognizes him one day in a store from the scent of his special aftershave.
- Sam and the team try to track down a new serial killer who castrates his victims and seems to be driven by feelings of public duty and legal responsibility. Meanwhile, John gets into trouble through no fault of his own for something that appears in the news about the case. Also, Sam finds herself attracted to Paul Sterling, the district attorney assigned to prosecute Donald Lucas.
- People who seem to have nothing in common are being killed in the Southeast USA. Grace's autopsy yields that all the victims has the same rare blood type. The team uncovers evidence that confirms all the victims were the children of Chris James Allmon, a Charles Manson-like cult leader currently incarcerated in a Georgia psychiatric facility. Sam interviews the adoptive parent of one of the remaining children and quickly surmises their son, Toby Watson, is the killer. She theorizes that he is killing his siblings to 'cleanse' himself of his deadly lineage. Meanwhile, Sam confronts her father, Walter Anderson, about his unethical experiments during the 1960s involving viral experiments that led to the mental breakdown of 34 people.
- George and Sam go undercover as IRS agents at Borden & Associates, a management office in Palm Beach, Florida, because five of the clientèle have been murdered with one finger from their left hand missing. As Sam profiles the most likely suspect, Bobby O'Hara, whom shows a strong interest in her, the firms shadowy security chief, Leo Cantrell, becomes suspicious of Sam's true identity. Meanwhile, Kevin Miller, an arrogant FBI agent working the case, complicates the investigation much to Bailey's worry for Sam's safety and Miller's indifference to otherwise, while John works with the local police detective, Lt. Cynthia Ford, in discovering the bodies.
- When Rachel visits her old college in Maryland to appear on a radio call-in show to discuss a series of ongoing sexual assaults on campus, the case takes a peculiar personal turn when the rapist repeatedly dials up to mock her on-air, prompting an ongoing mind game of cat-and-mouse between them. Meanwhile, Rachel finds herself drawn to an old boyfriend who is now married to her former roommate, Susan. Rachel also meets the therapist, Dr. Tom Arquette, assigned to her brother's drug rehabilitation. Also, George slips in his shaky bid to end his own addiction to painkillers by missing work and concocting excuses to Bailey and Grace to his whereabouts.
- At Christmas time, still recuperating from Coop's death at the hands of the serial killing couple Jack-and-Jill-of-All-Trades, Sam decides to attend a college reunion. There, Sam and Angel reunite with friends Colleen, Drew, Greg, Monica, Tracy, and Roy. An enjoyable holiday gathering quickly becomes a nightmare when Colleen is murdered and all the evidence points to Colleen's husband Drew, whom Sam never liked. Soon another friend, Roy, is murdered, and then Drew himself. Back in Atlanta, Sharon (a.k.a: Jill-of-All-Trades) strikes out on her own and murders a lingerie shop clerk. The team investigates and starts to make headway. When Sharon learns of Jack's obsession with Sam, she sets out to kill her.
- As Christmas nears, Rachel and the VCTF work into the night in search of a twisted serial killer who goes on-line to select his victims, all of whom are carefully screened, seeking a candidate he can make over into his ideal woman. Meanwhile, Rachel is surprised when her troubled younger brother, Danny, drops in from out of town and displays telltale signs of substance abuse. Also, Rachel finally confronts George about his own addiction to pain pills and other drugs.
- Rachel, Bailey and the team travel to Yosemite National Park where a maniac brutally kills a mother and her two daughters. While circumstantial evidence points to a local outlaw biker, Rachel constructs a different suspect profile, one who feels remorse and might have sibling issues. Meanwhile, George's lingering substance abuse problem causes a dangerous embarrassment for Bailey and the VCTF when they get the wrong address of a suspect, just as an attractive congresswoman, Nan Archer, begins an investigation of the unit, and she is most impressed by Bailey. Also, Rachel's budding romance with Tom, her brother's drug counselor, hits a snag when Danny finds out.
- While shopping in a convenience store with his girlfriend Kate, John intercedes during a robbery. When Kate is mortally wounded, Rachel and Bailey are concerned that he will mete out his own justice outside the law. Even John's shooting of one of the suspects in the robbery comes under review, prompting him to angrily resign and grapple with his overwhelming emotions of guilt for Kate's grave condition.
- Sam and Bailey get caught up in a jewel heist by a trio of mentally unbalanced crooks, named Randy, Kate and Stevie, that quickly turns into a hostage situation within the jewelry store. Sam and Bailey struggle to profile the perpetrators and their relationships with one another before any lives are lost. Sam tries to reason with the ringleader, Randy, to give up. Meanwhile on the outside the building, John quarrels with the pompous and overzealous police commander who wants to catch or kill all the perpetrators, even if it means that all of the hostages will be killed.
- When a series of random murder victims are found on the streets of St. Louis, Rachel and the VCTF team believe the killer is a military veteran who uses weapons of opportunity, and their focus shifts to an incoherent, ranting homeless person who fits the profile. However, Rachel wonders if she should widen her field of suspects to include any ex-serviceman, and trained killer, who is susceptible to an altered state psychosis. Back at VCTF headquarters in Atlanta, George ignores his increasing reliance on prescription pain pills while recovering from his minor car accident.
- Sam and Bailey work with FBI field agent Susan Marsh whom is tracking Robert Lee Gregg, a conservative civic leader in Atlanta whom is suspected in the killing of six gay men. But their investigation is happened by Susan's former boyfriend, Richard Russell, whom is stalking her. Susan insists she's in control of the situation, but Bailey thinks otherwise when her boyfriend is found murdered and Russell is a suspect. Things get worse when Russell targets Bailey and his ex-wife Janet whom are now back together. Meanwhile, Sam leaves the investigation and travels to Miami to investigate the disappearance of a local man who may be connected to the Gregg killings, and she finds herself being perused by Detective Mario Monagno whom still wants to date her.
- A serial killer who kills with his bare hands leaves the bodies of his male victims at the Brown Derby, the Trocadero, and other Hollywood landmarks. Sam profiles the killer as someone trying to rectify some trauma he experienced in his past. The team follows a trail of clues that eventually leads them to a rather ordinary cab driver who does not seem to have the strength necessary to commit the crimes. A search of the man's apartment yields evidence however, that matches Sam's profile to the letter. Sam soon realizes the man suffers from multiple personality disorder. Meanwhile, the imprisoned Donald Lucas continues to taunt Sam while George meets with Bailey where they discover that Sam's father, a scientist, participated in experiments that had deadly consequences.
- The day after Jack's clever escape from the prison, Sam must look into herself in order to find him. Everything seems to point to her childhood which reveals that Jack has apparently stalked her all his life. Then, Jack abducts an infant and tries to lure Sam into finding him.
- While Rachel continues to be stalked by the renegade Marks bent on emotionally destroying her, she and the VCTF team respond to a series of murders of wealthy men in Memphis who solicited sex from the same desirable woman and they suspect a jealous admirer may be to blame. Meanwhile, Grace must drop everything when she goes into labor and George is the only one there for her. Also, Rachel is proud when her brother Danny begins his new job on the loading docks, drug-free at last. But the situation is compromised when Marks begins stalking him too.
- The VCTF is called in to assist in a stalled investigation which revolves around a series of killings in Allentown, Pennsylvania in which the victims faces have been burned off. Sam is leery to intercede for her former boyfriend, Michael Westmore, who's leading the investigation. Sam and Bailey disagree about Michael's handling of the case. Whereas Sam feels her friend should be given some slack, Bailey feels the man's performance sub-par and should not be excused. Forensic evidence shows that the victims' eyes were the specific target to the killer. Sam uses her intuition and the evidence gathered to theorize the killer did not want to be seen by his victims.
- A series of murders across the Southwest leads Sam and the VCTF team to an unlikely couple: a 32-year-old woman, Josie Wells, and a 16-year-old boy, Alex Lopez, who apparently abducted her from her child's soccer field in Boulder, Colorado. Sam figures out that the woman was apparently the victim of physical abuse as a child and has abandoned her unhappy and lonely married life and reliving her glory days with the boy she met on a help phone line. Meanwhile, Bailey tries to reason with his ex-wife, Janet, not to remarry for he feels she's throwing her own life away.
- Rachel pursues a child killer who poses as a school photographer to pick his next victim.
- Sam and the VCTF team travel to Newark to investigate a series of killings where the killer cuts and hand off one victim, and the head off another. Sam accurately assesses the killer's pathology of being a young man whom is killing a variety of women by lashing out at those who remind him of his nagging, demanding mother, before he makes the final quest to kill her. Meanwhile, Sam realizes hat she and Chloe must begin a new life, and to that end at Angel's persuasion, decide to move into a new home.
- Fueled by the abuse they suffered as children, a brother and sister decide to save another child from the same unfortunate fate. To do this, the warped siblings kill the boy's parents as well as two others to make it look like a mafia hit. The VCTF investigates the mass murder and Sam immediately bonds with the abused boy, Peter. The parent has mob ties, so it is immediately assumed that their murder resulted from their illegal activities. Though skeptical of this scenario, Sam does not dispute it for that would result in Peter being held by the system until the murder is solved. Meanwhile, Sam's estranged father returns and the two try to heal their strained relationship.
- Sam and the team try to catch a mystic arsonist on the loose in Atlanta. Sam profiles that he apparently risks his own life by setting the fires himself on the spot. After a red herring lead involving a photographer always on the scene of the fires, Sam and the team find graffiti messages on walls of the burned out buildings in Farsi meaning 'fire god.' The man is apparently seeking a 'chosen one' immune to fire in order take him to the afterlife to meet his deceased wife. Meanwhile, Sam is worried about Chloe when she becomes emotionally withdrawn when one of her classmates becomes a victim in one of the fires.
- Rachel and Bailey respond to the growing list of isolated elderly men and women who are strangled while riding the rails in the Southwest, and Rachel notes cigarette burns that indicate the young killer must have been a victim of abuse as well. While the killer eyes his next targets, the VCTF theorizes that the dead victims must be surrogates for an angry drifter who feels rejected by society and taking it out on other derelicts. Meanwhile, Rachel begins to suspect George's painkiller addiction due to his increasingly erratic behavior while Bailey quarrels with the by-the-book Arizona Sheriff Cunningham over their investigation.
- An obsessed Bailey is haunted by an unsolved case in Georgia concerning several teen aged girls who were slain with a knife 15 years ago, and when more older victims are suddenly found, marked with slashes on their bodies, his focus zeroes in on their original prime suspect who has resurfaced in the area. Once Bailey has the VCTF team on board, he enlists Rachel's help to connect the two crime sprees but his decision to exhume the earlier victims understandably draws the wrath of their ever-grieving parents.
- A desperate Rachel and the VCTF team cast about wildly to quickly form a profile of an anonymous sniper who's perched atop the pump house of a dam with a commanding view of his victims in an adjoining park, but their options are limited out of fear that the shooter may have wired explosives that could inundate downtown Atlanta. While the body count rises, John risks his life to save some trapped patrons and Rachel suspects the murderer might be an enraged husband whose philandering wife is pinned down with her lover. Meanwhile, George fears for his job that Kim Doyle might permanently replace him and Grace worries about a problem with her pregnancy.
- When Rachel and Bailey investigate a series of Ohio murders in which the mutilated victims are cheating husbands, they suspect that the killer is the vengeful boyfriend of a woman common to all of the dead men... until she offers an unconvincing confession. Meanwhile, the VCTF team must contend with a local sheriff who wants to join their force, Grace must deal with her crumbling marriage and new pregnancy, and George is left limping after a painful car accident.
- Rachel and the VCTF team search for a serial killer who strangles women with knots of their own hair. But when the latest victim is the daughter of a powerful mob boss, names James Perrone, the FBI profiler must gain the grieving father's confidence to learn more about her habits. Meanwhile, Rachel is under pressure from the Bureau's Organized Crime Division director, Joel Marks, to take advantage of her access to Perrone and wear a wire to trick him into confessing to a fellow mobster's murder, thereby ending a lengthy investigation.
- Twelve women of a small Alabama town have mysteriously disappeared. When one of the missing is found dead, the VCTF begins an investigation which leads to the discovery of the remaining 11 women buried in a shallow mass grave. Once on scene, Sam is confounded when evidence points to a domineering, controlling pathology, other evidence points to a more passive one. When Bailey pressures her to narrow her profile, Sam's anxiety builds and she begins to question her own abilities. But it turns out that there are two killers, working as a team, each with different profiles. Meanwhile, Samantha tries to get a date with Paul Sterling, with less then successful results.
- Sam and George travel to his Minnesota hometown to investigate when someone is stealing the corpses of young, recently deceased Jewish woman. George and Sam learn that a Neo-Nazi group is active in the town. Though evidence points to the hate group, Sam feels the crimes are motivated by something other than anti-Semitism. This theory take shape when one of the two of the stolen bodies is found undamaged, with minor cosmetic changes made. Sam puts together a profile that characterizes the perpetrator as someone looking to create or re-create his vision of the perfect woman. Eventually, evidence points to a man who is insanely infatuated with a woman who works in his office. When the man kidnaps the object of his affection, Helen Jefferies, Sam fears he will attempt to 'immortalize' his vision of perfect beauty for all eternity.
- Now a member of the VCTF team, newly relocated agent/profiler Rachel Burke sorts through a series of murders where the killer singles out successful career women and subjugates them to humiliating housework and compulsive cleaning before posing them naked in kitchens or bathrooms. While Rachel narrows in on a suspect whose timid, fearful wife may be the missing link, she must first overcome her combative relationship with John who's increasingly skeptical to her methods. Meanwhile, Grace suspects she's pregnant again when she begins showing sings of morning sickness, and Rachel waits and waits for the movers at her new apartment to deliver her furniture.
- Rachel searches for a serial killer who does not seem to follow a pattern following the abduction of a 10-year-old boy from a local diner. Meanwhile, Bailey must testify before a congressional subcommittee to save VCTF funding which is threatened to be cut off by Congresswoman Archer. Also, Rachel finds that her apartment was broken into and an incriminating audiotape she made of Joel Marks bragging about setting up criminal suspects has reappeared in the court dockets where Marks vows revenge.