Mary McCormack stars as Mary Shannon, a U.S. Marshal working in the highly secretive branch of the witness protection program (WITSEC) who relocates Federal Witnesses - many of them career criminals, and many who are innocents that had the misfortune of witnessing a crime. They all have one thing in common - someone wants them dead. Mary's job is to see that doesn't happen, while at the same time attempting to manage her own dysfunctional family.
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.
ATF Agent Wade Guthrie is shot during an undercover weapons deal. When he wakes up, Wade learns he has been protected by Mary Shannon during his three-year coma. It is only his eye-witness testimony that can put a prolific weapons trafficker behind bars.
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. Meanwhile, Stan has to deal with an ex-boxer/witness suffering from pugilistic dementia.
When Dominic, a former sociopathic hit man with a love of explosives, falls in love for the first time, Mary fears that he won't handle rejection very well. Meanwhile, the WitSec office welcomes a new financial manager, and Mary says her goodbyes to Raphael.
When a hardened bank robber who's been in prison for decades is finally paroled, it falls to Mary to help him acclimate to life on the outside and keep him from falling back into a life of crime. Meanwhile, when one of Mary's other witnesses becomes the victim of a revenge plot, Marshall steps in to help out – only to find himself in a predicament when the witness prefers him to Mary.
FBI Agent Mike Faber returns to Mary's life when he gives her a new witness: Natalie, a key witness and co-conspirator in a nationwide mortgage fraud scheme which was operated by major gangs to raise millions for drugs and weapons. Mary is forced to work closely with Faber, who appears to have an alternate agenda: sparking a romance between the two.
Seth Mann, a legendary Marshal whose career spans decades and who also happens to be Marshall's father, comes to Albuquerque to work on Operation Falcon, a nationwide sweep of open warrants. Meanwhile, Brandi returns to Albuquerque with a suspicious story about her disappearance and a surprise guest connected to her past.
A woman from an organized crime family experiences a major health scare and witnesses her beloved niece repeating all of her mistakes. After she becomes vocal about her disapproval of her family's life, her cousin threatens her and she decides to take action and turn to the Feds. One problem: she has a secret that puts her status in Witness Protection in jeopardy, so she turns to the one person who can help – her new friend Mary Shannon.
A witness with Aspergers who has no social filter and can't lie stymies Mary, particularly when the witness refuses to testify against her only friend – the key conspirator in a numbers case. Meanwhile, Marshall and Stan race to figure out why an Immigration and Customs Enforcement agent is holding up the visa of a key witness before she is deported. Plus, Brandi reveals her plan for the money she made by investing with Scott.
Mary's newest witness is a homeless man who exposed a pipe bomb plot. As he struggles to conform to the rules of WitSec, Mary agrees to help him search for his birth parents – which presents unexpected problems when they are found. Meanwhile, Brandi becomes distrustful of Scott who once again needs money.
Mary plays "stepmother" to a rebellious 16 year-old witness of a jewelry heist whose separated parents are too self-involved to deal with their teenaged daughter's issues. Meanwhile, Marshall suspects that a witness has sold out his brother at a family reunion. Plus, Brandi takes care of Scott after he is assaulted under mysterious circumstances.
A priest, who witnesses the murder of a stripper, is all too eager to leave the priesthood when he joins WitSec but hesitant to cut off ties with the victim's family. Meanwhile, Stan struggles with telling a deceased witness's daughter the truth about her delinquent father. Also, Brandi decides to move in with Peter while Jinx returns and offers Mary some motherly advice.