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 ...
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.
When a hardened bank robber who's been in Witsec 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.
Mary is reunited with FBI agent Mike Faber, with whom she worked (and clashed) previously. This time the focus is on a new protected witness, Natalie Vickers, who assisted in a real estate housing scam that the FBI is investigating. Despite Natalie's entry into the WITSEC program, both Mary and Faber have their doubts about Natalie's commitment to the program when she seems to have no questions about how it will work - concerns that only deepen when she disappears and then reappears without explanation.
The members of WITSEC join other U.S. Marshals to help with an annual roundup of fugitives. This poses a problem for Mary's regular partner, Marshall, who is joined for this exercise by his father, who is also a U.S. Marshal (though not involved in witness protection) and very much "old school" - including the high standard to which he holds his sometimes sensitive, intellectual son. Then things become complicated when Marshall believes he recognizes one of his protected witnesses fleeing from a scene where several fugitives are apprehended.
Mary's new witness, Mia Cusato, comes to WITSEC with abundant evidence about the crime family of which she was a part. She confides in Mary, however, that she is dying of cancer and likely has only weeks or months to live - which may compromise her value as a protected witness. Marshall also struggles with the personal problems of one of his witnesses - a closeted gay man who has secretly brought his lover along into his new life in witness protection. Meanwhile, Mary's mother finally meets with Mary's and Brandy's half-brother Scott, one of the children from the new ...
Mary is assigned to protect a witness named Judy Wagrowski, whose extraordinary mathematical abilities allowed her to keep all the financial records of a numbers racket in her head. That skill, however, is the result of her Asperger's Syndrome, which also makes it difficult for her to understand figures of speech or to keep the secrets necessary to remain a protected witness. Judy also has trouble breaking her ties with Larry Silvers, one of the suspects she will testify against, whom she regards as her only friend. At the same time, Marshall and Stan try to help a ...
Mary helps her latest witness, a homeless man who's struggling with the program, find his birth parents. But the search could cause more problems than she anticipated. Elsewhere, Scott asks to borrow more money, raising a red flag for Brandi.
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. At a family reunion, Marshall suspects that a witness has sold out his brother. 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. Stan struggles with telling a deceased witness's daughter the truth about her delinquent father. Brandi decides to move in with Peter while Jinx returns and offers Mary motherly advice on dating.