While on a mission to locate an analyst in Moscow, FBI agent Will Chase runs into CIA operative Frankie Trowbridge. As they both endeavor to carry out their individual missions, circumstances lead them to work together.
As Will's past with Ray threatens the stability of the team, Will and Frankie try to stop an assassin from getting to the widow of an international smuggler, which forces Will to put his own comfort aside to go undercover.
As Frankie and Will disagree on the proper way to get the team accustomed to working together, the team is tasked to take down a neo-fascist group that possesses a chemical bomb.
Trying to retrieve nerve gas canisters from a Romanian warlord, Will and Frankie are forced to go undercover as a married couple to infiltrate the wedding of the warlord's daughter.
As the team investigates the deal of an American diplomat in England, Will and Frankie dance around their feelings for each other.
As Emma tries to help Ray mend his friendship with Will, the team stumbles upon a human trafficking ring and ends up caring for a kidnapped infant while trying to locate his family.
As a familiar face from Will's past makes matters complicated for him, Frankie deals with her feelings about Will and Emma's romance.
When the team is tasked with the transport of a dangerous prisoner, they are shocked when they discover the identity of their prisoner, who uses his inside knowledge of them to drive a wedge between the team members.
With Frankie distressed over her position in the team, she is forced to step up when Will is caught by an organ trafficking ring, leaving the team to scramble to save him.
When a tragedy hits too close to home for the team, Will goes down a dangerous path that threatens to swallow him whole, as Frankie struggles to figure out what to do.
When they learn about an engineering prodigy who is capable of building super weapons, the team pulls double duty as they try to convince him to join their side, while protecting him from others trying to get to him for his technology.
Despite Frankie's resolve to maintain her professionalism and leave no space for emotional responses, her meeting with a former guardian puts that notion to the test.
Ollerman makes a return, holding the life of one of their own as leverage to force the team to do his bidding. As they work to foil his plans, Frankie and Will have an epiphany about their relationship.