A man tries to kill himself in front of Jarod. Jarod learns he is a chemical engineer and that there are violations at the plant where he works which are being ignored. And Sydney runs into a man from his past at the Centre.
Jarod sends Parker and Sydney an invitation to join him at a school reunion. But on route Jarod meets a young man who wants to go home to make a special occasion so Jarod gives him his seat on the plane. Later the plane crashes and the man is killed. So he assumes the guise of a inspector to find out what happened. And upon arriving another inspector assumes that the pilot may have been at fault. But Jarod doesn't think so.
Jarod assumes the identity of a man whose son was kidnapped. And he tries to deal with the kidnappers. Later the man's head of security joins Jarod. While waiting for the kidnappers to call, Jarodtries to find out how the boy was kidnapped.
When Jarod gets a message from Sydney, to meet him at a small town. But when he arrives and asks for him, everyone in town acts strange. Eventually he is arrested by the Sheriff who then turns him over to Mr. Lyle who plans to turn him over to the Centre. Jarod learns that Lyle kidnapped the Sheriff's wife and placed her somewhere where she has limited life support. And just when Lyle was about to cut off one of Jarod's fingers, he is saved by his brother, Kyle. And they set out to find the Sheriff's wife.
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.