"The Operative" finds Madam Secretary playing defense against top security leaks from an undercover source named "Viper." The Secretary is caught by surprise when Viper reveals petty insults made by her very own staff about foreign leaders in their professional e-mails. These insults include some very playground style nastiness about France, a US NATO ally, from her own top-level staffer, Jay Whitman (Sebastian Arcelus). The Secretary is forced to go on an international apology tour (via video) and Whitman willingly offers his resignation.
If Viper's unveiling of international secrets wasn't enough, The Secretary also has to contend with a recent American captive called Schaffer, in Pakistan. It seems Pakistan is planning to execute Schaffer as a suspected spy, although Schaffer pleads that he is only an humanitarian aide worker.
Back at home, The Secretary's middle daughter, Alison (Kathrine Herzer), struggles through a romantic breakup. However, her parents can't comfort her, because then they'd have to admit that they learned about her breakup by having their iPad connected to her texts. It seems spying runs in the family.
Secretary McCord's husband Henry is approached by a high level Russian ambassador for a one-on-one meeting. Believing it's regarding his academic interests, Henry takes the lunch meeting, but soon finds out that the ambassador wants to use his status in exchange for an "A" for his daughter, who is one of Henry's students at Georgetown.
Henry, an ethics professor, doesn't take the bribe and is proud of himself for standing up to such a high level dignitary. Secretary McCord is proud of her husband as well, until she learns that Henry's ability to give good grades might be the only bargaining chip separating the young American, Schaffer, between life and imminent execution in Pakistan.
To save Schaffer's life, Secretary McCord goes against her own ethics, asking Henry to give the Russian's ambassador's daughter the "A", in exchange for the Russian's negotiation with Pakistan. Henry is noticeably upset. He never thought he'd be a pawn in his wife's White House job, no matter how high-level. When Henry refuses to go against his integrity to change the Russian student's grade, Madam Secretary is forced to get creative, eventually convincing Henry to give the Russian girl an incomplete so her record remains clean and her Russian Ambassador father uses his sway in Pakistan to prevent them from executing Schaffer.
Now Viper, aka Mr. Heller, is sick (in Guinea) after falling very ill. He wants to come home for treatment, but should Secretary McCord go out of her way to help the dissident who recently revealed high-level security secrets? Eventually, McCord's sense of duty forces her to fight even for Viper's life, pulling enough favors to get him back into the country, soon to face trial for espionage. Now that everything has worked out in America's favor, Madam Secretary feels comfortable allowing Whitman to stay on her staff. Whitman may have been a holdover from the previous administration, but he's McCord's guy now.
In a week of tough choices, the final tough choice is made at home. Secretary McCord and her husband Henry decide to stop spying on their teenage daughter, allowing Alison to make her own mistakes. They disconnect their iPad from Alison's texts, losing oversight over their teenager, but gaining a sense of ethics.