Kelly and Scott get an assignment not to their liking. They are sent to a seaside vacation spot to take out an undercover spy Karlovassi. But after meeting him they develop a friendship with the charming rogue.
Over the years, ten-thousand children have been kidnapped from a northern frontier province in Greece to be taken through the Iron Curtain. There they are brought up in state orphanages, brainwashed, and trained as agents to be later infiltrated back into Greece and used against their country. Robinson and Scott's assignment is to rescue a friendly agent involved with disrupting this child-smuggling operation but whom is now trapped behind the Iron Curtain.
Scott is ordered to get close to an African woman who has access to important intelligence about armed shipments to her country. But he is faced with an attack of conscience once he begins to develop genuine feelings for her.
A child violin virtuoso begs Kelly and Scotty to smuggle him out of communist Bulgaria so that he can live with his sister in Greece. Against better judgment they help the boy and get a nasty surprise for their trouble.
Ten days after Kelly has missed an important meeting held in Athens, Scotty finds him lazing on a quiet Greek isle in the Mediterranean. Kelly tells Scotty that he's "come in from the cold" - meaning he's quit the spy business.
While in a toy shop in Chinatown, San Francisco Kelly and Scott meet an attractive Chinese young woman named Mai Lin. Kelly is immediately attracted to her and strikes up a conversation. While showing her the sights they find it strange that she says she is from San Francisco yet has no knowledge of the most obvious San Franciscan sights...Alcatraz, Golden Gate Bridge, etc. The mystery gets deeper when they are assaulted and she is stolen away. Their investigation leads them to an ancient Chinese cult who have plans for Mai Lin.
In the American Midwest Kelly and Scott are on the run from an armed hunting party. They have learned the identities of some of the biggest saboteurs in America. They have been posing as ordinary businessmen and depend on their anonymity. Kelly and Scott seek refuge at a farm Kelly remembers from his childhood. The farm is run by Kelly's Aunt and Uncle whom he hasn't seen in over twenty years. They must all defend it when the farm is under siege from the armed gunmen.
In one of the final episodes of the series, Scott and Robinson relive how they first met, in a series of flashbacks. Back in present-day San Francisco, Scott has been hospitalized after a failed suicide attempt. He is recalling for the psychiatrist, Dr. Akivic, how he and Robinson collided, literally and figuratively, in their first days of training for the CIA. Later, the doctor interviews Robinson who recalls the same series of events from his point of view. Each of them tells of working on a training exercise with a third agent, Wally. They broke into headquarters ...
In San Francisco, Kelly and Scotty are on temporary duty at "the department's" training school. One of the trainees is a mole for the Soviets. After he kills another trainee, he gets permission to stalk Kelly and Scotty. The veteran agents end up accused and are on the run -- for real.
While sightseeing in a Mexican town Scott and Robinson think they see someone familiar. When they approach him he gets the drop on them and gets away. After checking they find out that Frank Hunter a convicted mental patient judged incurable and sentenced to life has escaped. Hunter is a demolitions expert who has sworn revenge against Tom Matthews, the agent who apprehended him. Matthews has retired and lives with his family in Mexico. Robinson and Scott are assigned to find Hunter and stop him before he can hurt Matthews and his family.
Robinson and Scott are on assignment at a beach side resort in Spain tracking down stolen rocket fuel. When their contact man is found murdered the boys are warned off by a beautiful woman. When they search his room they find a portrait of the woman. Using the name of the artist they track her down and discover she has the fuel and is going to trade it for her brother's freedom who is being held behind the Iron Curtain.
Ordered by their superior officers to check security on a general forced into retirement before the visit of a VIP, Kelly and Scott are thrown into a version of "The Most Dangerous Game" and are hunted as game animals.
Kelly and Scott are to be killed after they are used to test the authenticity of the appearance of a man who has surgically been altered to replace a senator that is to be murdered so the man as the senator can assassinate the president.
A series of leaks during the extraction of an asset cast suspicion on a Company friend of Kelly's. Kelly and Scott join the debrief team to discover which of the agents, Kelly's friend or another of Russian descent, is the traitor.
After the torture and death of a contact, Kelly and Scott take possession of the titular baby Carmelita in Guadalajara and go on the run to escape a gang in a black car who are convinced the infant is of great value.