Nanki-Poo, the son of the Mikado, assuming the disguise of a travelling musician, has fled from his father’s court in order to escape marriage with the elderly Katisha. He has fallen in love with the beautiful Yum-Yum but has been prevented from marrying her by Ko-Ko (her guardian), who also wants to marry her. At the beginning of Act One Nanki-Poo is hastening back to court Yum-Yum, having heard that Ko-Ko has been condemned to death for flirting. Nanki-Poo hopes that Yum-Yum will now be free to marry him. Nanki-Poo learns from Pooh-Bah and Pish-Tush that Ko-Ko has become Lord High Executioner, thus preventing his own sentence of death from being carried out. In fact, Ko-Ko is to marry Yum-Yum that afternoon.

A letter from the Mikado presents Ko-Ko with the challenge, the Mikado orders him to execute somebody or lose his position as Lord High Executioner. He is considering whom to execute when Nanki-Poo appears, intent upon suicide as he cannot marry Yum-Yum. Ko-Ko proposes that Nanki-Poo should marry Yum-Yum for one month and then submit to public execution. General rejoicing follows this solution, after which Katisha appears in search of her beloved Nanki-Poo. Driven away, she seeks an audience with the Mikado.

Synopsis - Act II

The blissfully happy Yum-Yum and Nanki-Poo are preparing for their forthcoming wedding. However, Ko-Ko arrives with the distressing news that, according to a law he has just discovered, when a married man is executed his wife must be buried alive, Nanki-Poo resolves to kill himself. This of course presents a further problem for Ko-Ko, as he will need to find someone else to execute. Nanki-Poo offers himself for immediate decapitation but Ko-Ko cannot perform the task, not wanting to be cause of Yum-Yum’s death but thinks of an alternative solution; Pooh-Bah makes a false affidavit that Nanki-poo has been executed and that Yum-Yum and Nanki-Poo prepare to leave the country.

When the Mikado appears Ko-Ko thinks that he has come to check up on whether the execution has been carried out, and so produces the affidavit and describes the decapitation in gruesome detail. In fact, the Mikado has come with Katisha in search of his lost son. When it becomes apparent that the person Ko-Ko has "executed" is the Mikado’s son, Ko-Ko and his accomplices are declared guilty of the dreadful crime of killing the Heir Apparent. They quickly explain the falsehood and produce Nanki-poo alive. Katisha, learning that Nanki-Poo has married Yum-Yum, isfurious. However, Ko-Ko resolves the situation once again by offering his own hand to Katisha who, after some persuasion, accepts him. The opera ends in general happiness and celebration.