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Marcus Luttrell and his team set out on a mission to capture or kill notorious Taliban leader Ahmad Shah, in late June 2005. Marcus and his team are left to fight for their lives in one of the most valiant efforts of modern warfare.

A scientist's drive for artificial intelligence takes on dangerous implications when his own consciousness is uploaded into one such program.

The first human born on Mars travels to Earth for the first time, experiencing the wonders of the planet through fresh eyes. He embarks on an adventure with a street-smart girl to discover how he came to be.

In spite of the apparent risk, a young and ambitious news reporter jumps at the opportunity to investigate a mysterious location in the New Mexico desert where people are disappearing.

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 as Jinx.

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 Ripp. 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.

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.

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.

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 New York. The Rabbi was sent by his wife, who wants a divorce, so he has to sign something. He refuses to do it unless his wife tells him herself. So she comes to New Mexico and he learns something she's been keeping from him which makes him unwilling to give her what she wants.

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 Mary getting shot while trying to protect Francesca.

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.

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 Rafael's mother from the Dominican Republic. She has made the trip to celebrate Mary and Rafael's engagement - even though Mary actually rejected Rafael's marriage proposal several months before.

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

A former high line thief from Boston tries to give up crime for the sake of his teenage son, and Mary and Marshall search for the person who nearly killed Mary in the season two cliffhanger.

A break-in threatens the security of the first witnesses Mary and Marshall handled together, prompting flashbacks to the way Mary joined WitSec.

An ATF agent is shot by a weapons dealer he was working on. He ends up in a coma and wakes up a few years later. He is told that he is now in the Witness Protection Program and Mary's in charge of him. He asks to see his girlfriend. Mary says she'll do what she can. Raphael's aunt comes for a visit and questions Mary about her plans with Raphael. The agent meets with the prosecutor who tells him that his partner, who at the time of his shooting was addictive to pain killers which made him unconscious when he was suppose to back his partner. So they need his testimony to put the man who shot him away. And it's not a good time for him to see his girlfriend. After he leaves, the prosecutor tells everyone including Mary that his partner and girlfriend are now married. They try to convince him to wait after the trial but he bolts to see her.

Mary and Marshall try to help FBI Agent Mike Faber convince his informant to enter WITSEC. Despite their best efforts, the informant refuses their protection and gets himself into a heap of trouble. After Mary, Marshall and Agent Faber save the informant from certain death, he and his family join Witsec. Meanwhile, Stan has to deal with an ex-boxer/witness suffering from pugilistic dementia.

When Mary's new witness, Dominic, a socio-pathic former hit man with a love of explosives, falls in love for the first time, Mary hopes he will finally have a shot at normalcy and redemption. Unfortunately, it all goes pear shaped when his would-be-girlfriend, Naomi, breaks Dom's heart. Mary races to stop Dominic from taking out his pain in the form of an explosive device meant for Naomi. Meanwhile Mary deals with her own regrets after her break up with Raph.