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'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 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 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 learns that her witness, a NCAA basketball star, has a gambling problem
The closeness of a family is tested when they enter the program after the daughter witnesses a shooting.
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.
Natasha, the mild mannered Ukrainian accountant, has gotten her new breasts, but her life becomes more complicated when she discovers that her new boyfriend is also in WITSEC.
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.
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.
Mary and Marshall find themselves in a difficult position when Stan's very first witness turns up dead and he is implicated in her murder.
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.
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.
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.
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.
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.
A world-class counterfeiter witness is suspected in a murder; Mary and Marshall realize they may be hiding a witness from the government.
When a Wall Street blue blood rats on his boss' investment fraud and hides out in WITSEC, something from his past life comes calling.
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.
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.
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.
Mary’s new witness falls in love for the first time; Mary must stop her witness from taking out his pain in the form of an explosive device.
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.
Mary's new witness is part of a mortgage fraud ring and is an important link in the case of FBI Agent Faber.
Marshall is being evaluated in the field by his father (Geoff Pierson) during a joint fugitive operation. Mary meets Brandi's secret friend.
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.
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 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 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.
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.
Mary is caught between a witness and a suspect.
A beauty pageant queen finds out that she's spent most of her life in witness protection
Mary works with an unapologetic con artist.
An Amish witness comes into the program and must learn to adapt.
A terminally ill father wants to reconcile with his children.
Mary plays marriage councilor in order to mediate a WITSEC divorce. Not only must she reconcile a stubborn witness, but also thousands of years of Hindu tradition, in order to save the case and keep a family out of danger.
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.
Marshall and Stan contend with a rock-star witness and her controlling mother while Mary is away on a WITSEC-mandated road trip.
Mary helps protect a guilt-ridden Army veteran; Marshall & Abigail consider the next step.
Mary protects a courtesan from the gangster father of her baby.
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.
With Jinx out of town and Mark busy with a last minute business trip, Mary has no choice but to head to work with Norah in tow. But when Mary arrives, Delia points out the obvious: Mary can't be with Norah and a witness at the same time. Meanwhile, Marshall and Abigail are trying to determine whether or not Kristi Owens should enter WITSEC and Associate Director Campbell gives Stan some surprising news about the future of the Albuquerque office.
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.
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, 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 is still reeling from the flood of emotions stirred-up after having to arrest her father, James, when he unexpectedly shows 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.
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.
Series Finale: Drastic changes take place at the Albuquerque WITSEC office. Mary finds herself caught between a witness and an unexpected family reunion.
