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.

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 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.

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.

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.