Hunter’s archenemy, a Soviet agent and killer known as Bluebird, is suspected of killing an American who betrayed the Soviets after leaking American nuclear secrets to them. Bluebird murders a succession of informants before Hunter can contact them, usually leaving a razor-sharp throwing star in each victim's body but on one occasion sabotaging a victim's parachute. The murders lead Hunter and Marty to a Soviet plot to discredit an American nuclear-powered electric plant design. This was the first episode of the weekly series, which used the new premise of Hunter and Marty being counterespionage agents.

A Soviet double of Hunter—created through the use of plastic surgery—arrives to carry out a plot to kill General Baker and frame Hunter for the murder. But first he has to fool Marty into believing that he is the real Hunter.

A mad scientist programs an American agent to kill Hunter. He then arranges for Marty to have a car accident so that he can treat her for her injuries and uses the opportunity to program her to kill her uncle, an influential admiral in the United States Navy, when she gets the news that Hunter is dead. Hunter uses a mirror to snap her out of her programming.

After a hitman dies during a car chase, Hunter switches wallets with him, takes his place, and sets out to find out who hired the hitman and who the hitman's target was—and soon begins to realize that he was himself the target of the hit.

After a witness for a United States Senate committee investigating a connection between organized crime and a U.S. government intelligence agency (the fictional "GIA") is murdered, Hunter and Marty face the challenge of convincing the last surviving witness that they can protect him if he testifies—and a retired song-and-dance man becomes a key figure in their search for the assassin.

In a flashback to before Hunter′s 1969 resignation from "the Agency" when he was still their chief of operations in West Berlin, Hunter becomes a wary ally of an East German spy who shot his fiancé to death nine years earlier. After the East German is killed at a film festival in Los Angeles, Hunter and the agency try to figure out who killed him.

Another flashback to the time when Hunter was still with "the Agency" as its chief of operations in West Berlin before he resigned in 1969. When Hunter, Marty, and Baker try to stop renegade American agents from assassinating a United States Government official, Hunter's adversary, seeking political asylum in the United States, offers to betray the group that hired him to assassinate the dignitary.

Dr. Martin Reed, a chemist working for the U.S. government, disappears mysteriously. At the same time, Dr. William Maklin, one of his associates, is killed in a plane crash. Investigating Maklin's death, Hunter discovers that Reed is in hiding and plotting to poison the Southern California water supply and kill two million people if he does not receive a payment of $10,000,000 within 48 hours.

When Hunter helps with the exchange of a U.S.-held Communist spy for a Communist-held American spy—who happens also to be his favorite instructor in spycraft—persons unknown intervene in the exchange and kidnap both of the spies being exchanged. Hunter and Marty are assigned to find the missing American spy, and Hunter begins to suspect that a traitor in his own agency is responsible for the kidnapping.