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.

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.

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

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

When Marshall's witness escapes from the WITSEC offices and disappears on an Indian Reservation, Mary and Marshall will need the help of a Native American detective to track him down.

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.

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.

Even with Joanna babysitting Norah and Brandi addressing her alcohol problems in rehab, things are still chaotic in Mary's life. Douglas Hampton/Harvey, a drag performer who was known as Kandy back in New Orleans, joins the program after accidentally interrupting a drug deal between a club manager and a member of a dangerous drug cartel. The team tells Douglas that he must leave Kandy and his performance act behind, but the frustration of his new life sends him back onto the stage and into the spotlight.

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.

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.

Mary is caught between a witness and a suspect.

Mary works with an unapologetic con artist.

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

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.

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.

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.

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.

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.

A world-class counterfeiter witness is suspected in a murder; Mary and Marshall realize they may be hiding a witness from the government.

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's assignment this week is Treena Morris a con-artist who is married to a diamond smuggler. After she is arrested by the feds, she decides to tell all on her husband and his friends. While Mary is trying to keep her safe, Treena gets engaged and her photo is all over the papers.

Mary works to solve the mystery of who tried to kill her witness, an art dealer. To complicate matters, both his mistress and his wife are in the program…and key suspects.

Mary briefs a new witness whose visitation rights with his son depend on the man's testimony. When Mary learns the boy is missing, she tries to find him.

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

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.

Mary protects a courtesan from the gangster father of her baby.

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 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.

When a Wall Street blue blood rats on his boss' investment fraud and hides out in WITSEC, something from his past life comes calling.

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.

Mary keeps an eye on a teen witness whose separated parents are too distracted by their own issues to pay attention to their daughter. Marshall thinks a witness may have betrayed his brother; and Brandi tends to Scott after he's attacked.

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.

The closeness of a family is tested when they enter the program after the daughter witnesses a shooting.

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

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 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.