Everyone survives the bomb blast that ended the season 2 finale. There is no rational explanation given as to how everyone survived. Sydney is temporarily blind as a result of the explosion. Gar's body is planted in the rubble so he ends up being blamed for the blast instead of Sydney. Jarod fakes psychosis to gain admission to a psych hospital where he tries to solve a murder. The Triumvirate sends someone to assist in Jarod's capture. Miss Parker learns the identity of her twin brother.
Jarod is contacted by a Native American with information to help him in his search for his father, but soon finds himself in a race to find him before a gang of bounty hunters track him down, and then help him resolve a case of local land corruption. Miss Parker's attention also shifts to searching for Jarod's father, but for a less benevolent reason. Sydney's sight begins to return.
Jarod recognises the MO of a new kidnap case from one he worked on years ago at The Centre. He becomes a criminal behaviourist from the justice department and enlists the assistance of the convicted psychopathic killer from the earlier case to help rescue the kidnapped girl before she is killed by the copycat killer. Miss Parker, Sydney and Broots continue to peruse Jarod under the continued interference from Mr Raines.
Jarod falls for a wealthy restaurant owner who shows compassion for an out-of-work family, but their paths cross again when the corrupt business man he is there to expose turns out to be her husband. Things become even more complicated when the business man is killed in a house fire. Meanwhile, Jarod sends a clue to Miss Parker at The Centre leading to a new discovery about Mr Lyle's past.
When Broots is sent to The Centre Data Annex to investigate an information leak The Annex is attacked by a masked gunman who kills all the staff. Broots manages to escapes but soon becomes a hunted man as Mr Lyle takes steps to seal the leak - no matter who it really is. Jarod races to protect Broots from The Centre and from the gunman "Damon", who has a history of stealing Centre secrets for evil use.
Jarod is pretending to be an ex-convict to find out what happened to another parolee. And it might involve a parole officer who makes his charges commit crimes. Sydney also learns that the husband of the mother of his son is dying and goes there for support.
Jarod becomes an ATF agent to help Sydney's son. It seems he's in the Appalachian Hills with some other people when they are taken captive by a paramilitary group. Sydney does what he can to help and learns that the Centre is behind the whole thing.
Jarod becomes a professor of a criminology class whose former professor has mysteriously gone missing leaving behind his pregnant wife. He leads the class to explore and reveal the sinister truth of his disappearance.
A man named Mr. Lee is hired by someone at the Centre to locate Jarrod. After looking through all of Jarrod dsa's and notebooks, he tells the one who hired him that he needs to speak to 7 people who were in contact with Jarrod. So the Centre brings 7 people to him and that's when he speaks to them and eventually gets a line on Jarrod.
Jarod goes to Atlantic City to help Argyle pay-off a debt to Sonny Faddis, a local loan shark. Argyle has been trying to fund a trip for his father to see the Pope. But they soon get drawn into a turf war between Faddis and another local loan shark, Dennis "The Cuban" O'Quinn. Miss Parker, Sydney and Brooks, returning from Hawaii on a Centre jet, get delayed in a storm and Miss Parker tells Sydney about her feelings for Thomas, the man doing some work on her house.
Jarod tries to locate a career criminal who happens to be the biological father of a boy in desperate need of a kidney transplant. Meanwhile, Miss Parker and Broots continue their efforts to locate Jarod.
Jarod becomes a radio talk show host to track down a violent caller with ties to an Army program that used dangerous chemical agents on unwitting human subjects. Meanwhile Thomas invites Miss Parker to move with him to Oregon.
Miss Parker wakes up to find Thomas brutally murdered. At first she's a suspect, then the murder is pinned on some junkie patsy. As usual, all roads lead back to The Centre when it comes to the real culprit(s).
Jarrod who's currently pretending to be a cop and when he's done was about to leave, when word gets out that a boy has been kidnapped which sparks Jarrod's thoughts of his being taken away from his family. So he decides to stay on to work the case. Jarrod then learns the FBI is getting involved cause it seems the boy's abduction is similar to a couple of abductions that occurred years ago. So the VCTF team arrives and Jarrod finds himself working with Profiler Samantha Waters, who doesn't get a good vibe of Jarrod.
When the Centre learns where Jarod's father will be, they send someone to take care of him. Angelo who overheard the conversation gets word to Jarod who then races to save his father. Only problem is the place is an arctic station and once he arrives, they're trapped and one of the people there is the Centre's assassin and he starts killing off everyone.
Jarod continues to follow a trail to find his father, but Brigitte always appears to be one step ahead. Meanwhile Miss Parker investigates a revived center project ominously called "Gemini" that her mother had opposed.
Jarod and his father team-up in a bid to rescue his clone from the center. A senior representative from the triumvirate makes his presence felt at the center, the balance of power falters, old secrets are revealed and lives are in jeopardy.