Number Six is persuaded to participate, as the white queen's pawn, in an oversized game of chess using people as pieces. A rebellious rook is taken to the hospital for "evaluation". After the game is completed, Number Six talks with the Chess Master, who comments that one can tell who is a prisoner and who a guardian "y their disposition. By the moves they make." Number Six is later invited to visit the hospital to observe the fate of Number Fifty-eight, and sees him subjected to Pavlovianmind control treatment. The woman playing the queen, who had fraternised with Number Six during the game, is subjected to hypnosis to make her fall in love with him and report his whereabouts should he attempt to escape again. Number Six shuns her, but seeks an alliance with Number Fifty-eight and other villagers that he now believes he can identify as prisoners, not guardians. They attempt an escape by making a two-way radio out of various pilfered electronic parts and then hailing a passing ship with a Maydaydistress call, pretending to be a crashing airliner. Number Six discovers, however, that again he has been a pawn — Number Fifty-eight had mistaken the strong-minded Number Six for a guardian. Believing that the escape attempt was a test of his loyalty, he reported it all to Number Two.
"Checkmate" was the third episode to be produced, following on from "Free for All" the second. As in the prior episode Number Six states he intends to find out "who are the prisoners and who are the warders", it could be inferred that in "Checkmate" he is belatedly putting this plan into action. As this was an early episode in production, there is a reference in "Checkmate" to Number Six being "new" in The Village. The episode's original title was to be "The Queen's Pawn", a play on the fact that Number Six had recently been in "Her Majesty's service". At the beginning of the episode, the lawn is seen uncovered by chessboard squares; a few moments later, it is shown as the chessboard. The chessboard remained in place for a week during September 1966 during filming of this episode; when it was removed, the grass had been lightened and the pattern is clearly visible in prior episodes. The chess game is recreated annually by enthusiasts of the programme at their annual convention, held at Portmeirion.
Apart from the obvious metaphor that life is a game of chess, the episode deals with conformity and pressures to conform, particularly peer pressure. Parallels have been drawn with the Milgram experiment, Asch conformity experiments and the Stanford prison experiment. Similar techniques are used to make Number Six conform, hoping he will reveal the secret of his resignation. However, Number Six discovers, as usual, that his trust is misplaced and the distinction between prisoner and warder remains blurred. The piece played by Number Six in the chess game is the same as that played by Alice throughout the story in Lewis Carroll's Through the Looking-Glass — White Queen's pawn.