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.

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

In 2003 Mary meets Marshall for the first time as they get lovers CLAUDIA TOBIN and HENRY DOER into the WitSec program, and it's a toss-up whose relationship is going to last: Claudia and Henry's, or Mary and Marshall's.

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.

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.

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

A building collapses on one of Mary's witnesses, leaving him exposed to outside threats, so Mary has to risk her life in order to keep her witness safe.

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.

An engineer blamed for a bridge collapse enters the program after being targeted by angry family members of the victims who died in the tragedy.

Mary helps protect a guilt-ridden Army veteran; Marshall & Abigail consider the next step.

Mary protects a bigamist not only from his former employer, but also his two wives. In WITSEC, cheating the black market can be dangerous; but cheating on multiple wives is a death sentence.

Mary is still reeling from the flood of emotions stirred-up after having to arrest her father, James, when he unexpectedly showed up on her doorstep after being AWOL for 30 years. Bad goes to worse when Special Agent Robert O'Connor, Mary's "favorite" FBI agent, demands her assistance to get James to provide critical information regarding his old partner-in-crime, Cormack “Sully” Sullivan, one of the FBI's 10 Most Wanted.

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.

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.

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.

Mary lends her expertise for the U.S. Marshalls by making a training video with a film crew. Elsewhere, Marshall prepares the arrangements so that an elderly mobster in Witsec can go to his son's funeral.

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

Marshall is being evaluated in the field by his father (Geoff Pierson) during a joint fugitive operation. Mary meets Brandi's secret friend.

Mary is caught between a witness and a suspect.

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

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.

Mary tries to help a parolee acclimate to life outside of prison after having spent 38 years behind bars while Marshall helps out when one of Mary's witnesses no longer wants to work with her.

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.