When The Mikado begins, a wandering minstrel named Nanki-Poo arrives in the town of Titipu, searching for a beautiful young maiden named Yum-Yum. Nanki-Poo met and fell in love with Yum-Yum earlier, but found that she was betrothed to her guardian, a “cheap tailor” named Ko-Ko.  Recently, however, Nanki-Poo has learned that Ko-Ko has been condemned to death for flirting, according to a decree of the ruling Mikado that any man caught flirting with someone other than his wife is to be executed.  Anticipating the death of his rival, Nanki-Poo has come to claim Yum-Yum for himself.

Unfortunately, Nanki-Poo learns that the town of Titipu has cleverly averted the cruel decree of the Mikado by naming Ko-Ko the local Lord High Executioner, reasoning that he cannot execute anyone until he first cuts off his own head, which he is unlikely to do.   All the officials in town have resigned rather than serve under a common tailor--except for the extravagantly snobbish but even greedier Pooh-Bah who has “mortified his family pride” by taking on all the town offices himself—along with all of their salaries.

Ko-Ko arrives and sings his famous (and often varied) song about all the people who “wouldn’t be missed,” if he should decide to reinstitute executions in Titipu.  He is keeping “a little list,” he confides, and there will be no shortage of appropriate victims, from “lady novelists” to “people who eat peppermint and puff it in your face.”

When Yum-Yum and her schoolgirl friends, Pitti-Sing and Peep-Bo, come upon the scene, along with a chorus of giggling maidens, Nanki-Poo confides to Yum-Yum that he is really the son and heir of the Mikado in disguise.  He has run away from court to escape an elderly lady named Katisha who has mistaken his common courtesies to her for declarations of love.

Suddenly Ko-Ko receives news that unless an execution is carried out forthwith, Titipu will be reduced to the status of a mere village, which would bring ruin to the town.  While his friends Pooh-Bah and Pish-Tush suggest that Ko-Ko, the only resident of Titipu who is already under sentence of death, should execute himself, Ko-Ko finds a “happier” solution.  He discovers Nanki-Poo in the act of trying to commit suicide because he cannot marry Yum-Yum. The two agree that Nanki-Poo will be permitted to marry Yum-Yum for one month and then will be executed; Ko-Ko may afterwards marry the widow.

Just as the town is about to celebrate the wedding of Nanki-Poo and Yum-Yum, however, an infuriated Katisha appears, claiming that Nanki-Poo is betrothed to her.

In the second act, the Mikado himself arrives to further complicate the plot.  Ko-Ko, Pitti-Sing and Pooh-Bah fall all over themselves trying to prove to the Mikado that an execution has been performed, as ordered (despite the fact that Ko-Ko has now realized that he is too softhearted to execute anyone).  However, the Mikado is actually searching for his escaped son, who, it is said, is traveling under the fictitious name of “Nanki-Poo.”   Katisha then discovers, to universal horror, that the name of the supposedly executed victim on the false affidavit the conspirators have prepared is “Nanki-Poo.”  

The only salvation for the conspirators and the town is for Nanki-Poo to “come alive” again.  But Nanki-Poo refused to “come back to life” unless Ko-Ko courts and marries the “appalling” Katisha so that Nanki-Poo can safely be with his Yum-Yum.  Ko-Ko, facing a choice between being executed for killing the heir to the throne and marrying a dragoness, gives in to marriage with good grace and the entire town rejoices.