In the first episode we meet Mary Shannon a US Marshall for the Witness Protection Program. In this episode Mary tries to figure out what went wrong when a mobster's son who was under her protection is killed.

Things get complicated when Mary takes on the case of Leo Billups. Leo saw his mother murdered and is going to testify against the people who killed her including his father.

Mary and Marshall take on a case involving Horst Vanderhoff, an agent for Lola, who's an assassin for hire. While trying to line up her next job, Horst is busted and agrees to testify against her to become a part of the Witness Protection Program.

Mary learns that her witness, a NCAA basketball star, has a gambling problem

A member of the Program under Mary's watch is in a car accident and Mary has to find out if it was an accident or related to his former life.

Mary suffers the consequences when an attractive witness, who she slept with, is accused of murder.

After watching her mother audition for "Sweet Charity" Mary is kidnapped; in New Jersey, Brandi's boyfriend Chuck is abducted and two FBI agents are killed; when federal agents suspect a connection, a nationwide manhunt ensues.

The family regroups after Mary's ordeal; Stan and Marshall search for a way to force Spanky to tell the truth about Chuck's drug trafficking; the FBI corners Mary in her driveway with Brandi's suitcase full of meth in the back of her car.

Season 1 Finale

A dead witness causes Mary to take leave of her administrative duties to solve a "Ten Little Indians" story, until her plan gets changed by her own brand of Post-Traumatic Stress disorder.

A northern California marijuana mastermind cannot testify without using the drug to neutralize his anxiety disorder.

A witness finds herself having difficulty in managing her own brood of children, so Mary offers to babysit the trio of problem kids.

An Orthodox Jew enters Witness Protection, but his wife refuses to join him. The situation is made more complicated by the fact he is being pursued by a man motivated by a higher authority.

When a series of murders seem to follow a new ex-con witness, including stabbing Mary's friend, she and Marshall have to figure out if he's the killer in time to save his next victim.

FBI agent O'Connor arrests Brandi on charges of drug trafficking and murder. Insisting her sister is innocent, Mary works to help Brandi while ultimately trying to discover O'Connor's real motive for his actions.

The barely legal daughter of Mary's witness – a Miami racketeer – finds herself in a dangerous romance, just as Raph's mother visits to prepare an engagement feast for the surprised Mary.

The US government helps a Latina political activist hide in Witsec, but the arrangement sours after she moves into her new home.

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.

ATF agent Wade Guthrie is shot and left for dead by gun trader Jasper Malone. After three years in a coma, he wakes to find the world he left behind has drastically changed.

A woman wants to escape from her family, who are heavily involved in organized crime, but a secret from her past puts her eligibility for the Witness Protection program in jeopardy.

After a priest witnesses the murder of a parishioner, he will have to give up his special vocation in order to enter WITSEC.

Mary uses a thief to catch a thief when she asks a witness to consult on a crime in order to exonerate Brandi of grand theft auto.

Mary's paranoid witness wants to reconnect with his son.

A beauty pageant queen finds out that she's spent most of her life in witness protection

Mary gets a WITSEC two-fer, when a witness is forced to enter the program after being mistaken for his "evil" twin brother. Not only must she protect the pair from their enemies, but also from each other.

Mary must protect her least favorite witnesses on the day of her sister's wedding.

Mary sees whether she can balance motherhood with a demanding profession and a dysfunctional home life, or if she will put her baby up for adoption.

Having slipped through the fingers of the FBI, James Shannon is on the run again and heading for the border, but first he must stop to take care of a little unfinished business. Agent O'Connor, convinced that she was somehow involved in James' escape, places Mary under investigation, but when he refuses to listen to her suggestions about the possible whereabouts of her father, the manhunt ends in tragedy.

Series Finale: Drastic changes take place at the Albuquerque WITSEC office. Mary finds herself caught between a witness and an unexpected family reunion.