If there's one thing witnesses & Wit Sec inspectors share, it's daddy issues. Or so Mary & Marshall realise when they meet witness Ben Kulpak. Angry with their father for the mistakes that landed him in this mess, his grown kids refuse to come into the programme with him. But when Ben winds up in the hospital & the Lithuanian mobsters after him manage to track down his kids, everyone's plans change. Tom & Cecile agree to join the programme & soon arrive in Albuquerque, but unfortunately it's a less than joyous family reunion — in part because there's some deserved resentment on their side for his wrongs as a father, & in part because it turns out that Ben has another secret he's trying to keep from his kids: he's dying. ...

When Dr. Amit Kishore, a well-respected neurosurgeon, runs afoul of the law by conspiring with the Indian mob to commit Medicare fraud, he cuts a deal & enters Witness Protection with his family. Unfortunately, the now-Kumars are not exactly one big happy family, & not long after their arrival in Albuquerque, the formerly docile Mrs. Kumar makes a shocking request: a divorce. Things get messy for the Wit Sec team when Ashok & Sudha (as they're now known) battle over the children, & an arrogant U.S. Attorney with a grudge against Stan pressures the team to keep the feuding couple under control. Though Mary & Marshall do their best to help the Kumars find common ground, it's anyone's guess as to how this story will end. After all, as Mary knows better than anyone, life is full of surprises: sometimes you get to start over, & sometimes you get pregnant. ...

It's a story as old as time, or at least as old as the story of Cain & Abel: two brothers turn out as different as can be, & can't seem to find a way to get along. Throw in a connection to an inter-state fraud operation, an FBI bust, & a subsequent relocation to Albuquerque, & you've got family drama of Biblical proportions. Meet George & Billy Stone. George is fastidious, Billy is fast-living. George is upstanding & responsible. Billy is... a mess. & now, thanks to Billy's involvement with some unsavory counterfeiters & a case of mistaken identity, both brothers have been dropped in Mary & Marshall's backyard. Billy adores his brother & is desperate to stay together; George's feelings towards his ne'er-do-well younger sibling are less warm. Even if Mary & Marshall can keep the brothers from killing each other, they've still got the angry thugs back in California to worry about. ...

With Mark co-parenting, Jinx playing babysitter & Brandi day-trading with their half-brother in Florida, Mary is finally ready to return to work for the first time since having baby Norah six months ago. WITSEC's latest witness is Ivan Gunter, a college student & a member of an elite eating club that runs a gambling website. When Ivan witnesses Brockton Jr., the president of the eating club, murder a fellow member, Ivan knows that he & his mother are in serious danger & in need of WITSEC's help. ...

With Jinx out of town & 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 & a witness at the same time. Fortunately, as Mary soon learns, Delia, Stan & Marshall make pretty good babysitters. Mary's first meeting of the day is with Beth Wilcox, a doll collector who entered the programme five years ago. Beth's landlord has been threatening to post a video of her on the Internet, which Beth & Mary both know could be a problem for Beth. Mary sends Delia to evaluate the situation at Beth's apartment so that she can check in on Carlos Ramirez, an alpaca farmer, who is worried someone from his previous life may have spotted him in town. ...

After John Arnett/ Wilson has a bad encounter with a doctor that harvests organs, he, his wife, & his two children enter WITSEC. At first, Marshall thinks John & his family are charming, but not surprisingly, Mary thinks they're creepy. & as usual, it turns out that Mary is right. Less than a week into the programme, the team discovers that John has a second car, house, wife & daughter – in other words, a second life. As a result, Mary & the rest of the team end up having to keep not one but two families – who just found out about each other – safe & happy. ...

Even with Joanna babysitting Norah & 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 programme after accidentally interrupting a drug deal between a club manager & a member of a dangerous drug cartel. The team tells Douglas that he must leave Kandy & his performance act behind, but the frustration of his new life sends him back onto the stage & into the spotlight. ...

Mary — who just arrested her father & delivered him to the FBI — must toughen up when she learns that her father is willing to provide the FBI with valuable information about his former partner, Cormac " Sully" Sullivan. He is only willing to provide the information, however, if three conditions are met: his sentence is reduced, he is put in a special WITSEC cell, & he gets to speak to Mary. They decide to set up a meeting between Sully & James in order to get Sully, but before they do so, the WITSEC team must locate both of James' families since Sully knows where they are. Much to Mary's frustration, Jinx & Brandi can't be reached & Scott refuses WITSEC's help. Later, things take a turn for the worse when Sully doesn't show up for the meeting & instead finds Scott & shoots him. & a stunned James, who Mary just learned has cancer, is placed in an ambulance, but manages to escape it. ...

James, Mary's father, has the entire WITSEC team & the FBI on a manhunt. While they are busy trying to locate him, James, the clever man that he is, manages to make his way to New Jersey where he gets revenge for the death of his son. & later, he pays Jinx a visit in Florida where he apologises for his past wrongdoings. Back in Albuquerque, Mary & Delia are tailed, which leads Mary to believe that Sully's men have found her. However, as Mary soon learns, the men actually work for Agent O' Connor who is convinced that Mary is working with her father. ...

Jinx & a pregnant Brandi reunite with Mary in Albuquerque so the family can deal with James' death together. While Jinx focuses on hosting a party, Mary must figure out how best to honour her father & what to do with the suitcase full of money he left in her basement. At work, Mary must help her witness Casey Lane/ Barnett, a former model with a drug habit, figure out what to do with her life. Also, Mary learns that Stan has been promoted to Deputy Director & Marshall has been appointed Chief of the Albuquerque office. While everyone is excited by the news, it means that Stan will have to move to Washington & possibly leave Lia behind. ...