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 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 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.

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.