The secret US abduction of a suspected terrorist from his Middle East homeland leads to a wave of terrorist attacks in New York. An FBI senior agent and his team attempt to locate and decommission the enemy cells, but must also deal with an Army General gone rogue and a female CIA agent of uncertain loyalties.

The second season, like the first, follows two different timelines. The primary timeline follows Patty, Ellen, and Tom as the firm goes up against an energy company who have engaged in unethical practices. A former lover of Patty's, Daniel Purcell, brings the matter to her attention, but then inexplicably backs out, leaving Patty up against UNR CEO Walter Kendrick and his fierce lawyer Claire Maddox. Meanwhile, Ellen works with the FBI to bring down Patty, while also seeking revenge on Arthur Frobisher for his presumed role in her fiance's death. Ellen is unaware that Patty is suspicious of her, and that Frobisher's criminal connections appear to extend to her new friend Wes.

A second timeline takes place six months later, when Ellen meets with an unknown person in a hotel room, and subsequently appears to shoot them.