Mary is placed on administrative leave pending the investigation of the FBI's raid on her house at the conclusion of the previous season. (The FBI unsuccessfully searched Mary's house for the drugs that her sister Brandi was holding for Brandi's boyfriend, Chuck.) While on leave, Mary's cases are given to Marshall, but Mary is allowed to work unofficially -- as Marshall's deputy -- when one of Mary's witnesses, who had been taken into the program 17 years earlier, dies under mysterious circumstances.

Mary tries to cajole a reluctant marijuana grower (and user) to testify against his former partners who are being prosecuted for the murder of a DEA agent six months earlier -- or else he and his family will be dropped from the WITSEC program and he'll be prosecuted for the murder. In the meantime, in the continuing fallout from the investigation of Brandi's possible drug possession and Mary's kidnapping, Mary is shadowed by a psychologist who will determine whether Mary can be returned to full status with the Marshal's Office.

A woman with three children who tries to find a man who can take care of them, hooks up with a criminal. When the man is arrested and she agrees to testify against him, so she enters the Witness Protection Program under Mary's supervision. When she continues to get a man, her eldest son is tired of it and Mary offers to help him get emancipated.

One of Mary's witnesses, an ex-mercenary who was supposed to testify against a former partner who killed 17 innocent people while assassinating a Mexican kidnapper, is trapped in the rubble of a collapsed building. Mary manages to reach his side and tries to keep him alive, in part by providing him with medical aid, and - because his face has been shown on television - by shielding him from other mercenaries who might target him while he is trapped. In the meantime, Brandi tries to apologize to Peter Alpert, the coordinator of the AA group whom she deceived by posing ...

A Jewish man from New York who, wanting to raise some money so that he and his wife could start a family, went into business with some Albanian criminals and used his father in law's business as a cover. But when the FBI assumed his father in law was the one associating with the Albanians and came to arrest him, he came forward. But his wife shunned him. He entered the Witness Protection Program and spent most of his time longing for his wife. One day he informs Mary that someone is following him. She learns that he was not sent by the Albanians but is a Rabbi from ...

The Albuquerque P.D. finds a body buried and with it Stan's old id. When Stan arrives he says he thinks the body was the first witness he handled: a comedian named Willie Rip. Willie was performing in a club owned by criminals at that time and saw them kill someone. The criminals were about to kill him when his girlfriend Gwen saved him, and following this they both entered the witness relocation program. Stan misses out details of Gwen when re-telling the story for Dershowitz. And when Dershowitz asks for the man's file, Stan withholds part of it.

Marshall is assigned to handle the case of Norman Baker, an engineer who designed a bridge that later collapsed. Baker testifies against Karl Hogeland, the head of the construction firm that built the bridge, but Hogeland and several relatives of those killed in the collapse still threaten Baker's safety. After a year in the WITSEC program, however, Baker continues to be obsessed with proving that the collapse wasn't his fault. In the meantime, Brandi continues to be pursued by Peter Alpert, whom she met while covering for her mother at AA.

Mary's witness, Dennis Stewart, testified against another convict in a prison stabbing case. Mary gets Dennis a job in a flower shop owned by her friend Colin, an ex-biker. When Colin gets violently stabbed at work one day, however, Mary and Det. Dershowitz reluctantly begin to wonder if Dennis, despite his mild persona, might have been capable of this crime - particularly when some unexplained stabbings show up in his past. While this is going on, Jinx and Brandi receive a visitor who brings them startling news about Jinx' estranged husband.

Months after the investigation of Mary's kidnapping, and the FBI's unsuccessful raid seeking methamphetamine at Mary's house, the FBI arrests Brandi on drug charges stemming from that investigation. Wondering where the FBI got new information to bring the charges, Mary asks Stan's help to sweep her house for bugs, and they discover a device planted in one of the walls. Mary learns that the young woman who recently came to visit Jinx might be her half-sister - but suspects that that woman might actually have been part of an FBI ruse.

Mary's newest witness is a security officer from Chicago named Ed Fogerty, who becomes enraged when told that his placement with WITSEC means that he cannot have visitation with his son Miles. Not wanting Ed to bolt from the program, Mary and Marshall try to arrange for Ed to have visitation with Miles that is supervised by the Marshal's Service. But they discover that the address and telephone number for Ed's ex-wife seem to be phony - and then become bewildered as they gradually conclude that Ed's son never existed.

Jesus Moreno, a former lieutenant to a Miami crime boss, enters the WITSEC program after his wife is gunned down by his former employer's gunmen. Accompanying him into the program is his 18 year-old daughter Olivia, who also witnessed her mother's murder - and whose rebellious behavior creates regular conflict with her father. The plans for Moreno's upcoming testimony against his former boss are hobbled, however, when Olivia disappears on the eve of the trial. As Mary deals with the problems in the Moreno family, she is also confronted with a surprise visit by ...

Someone from Washington comes to New Mexico to shoot a new U.S. Marshalls training video and they are instructed to give the director any help they can. And Mary balks at it so Marshall offers to be the technical advisor but when he learns that the son of one his witnesses, Joseph Tancredi has died, he has to go tell him. Joseph wants to go to the funeral but WITSEC rules forbids it. So Joseph decides to leave the program. Marshall then decides to use his vacation and accompany him to Chicago. Mary in the meantime is not being a team player with the director.

A master counterfeiter goes into Witness Protection after she discovers her girlfriend and partner in crime cheating on her with one of her male business partners.

A Wall Street fund manager entering WITSEC with his wife wants to give away all his assets, amounting to $137-million.

A special witness is brought to WITSEC - a woman from Latin America named Francesca Leandra, who barely escaped assassination in her home country because of her political activities. The State Department asks that WITSEC assign Mary to her full time, and Mary initially likes staying in the palatial home the government has found for her. But Francesca rebels against the opulent surroundings, and insists upon relocation to the most crime-ridden part of Albuquerque. This leads to a series of confrontations with the gang members in that part of town - and eventually, to ...