Act One

The lights rise on the mahogany and neon town of Titipu, where the zoot-suited gentlemen of Japan are swinging, scatting and living their lives in song ("We Are Gentlemen of Japan"). They are interrupted by the entrance of Nanki-Poo, a fresh-faced rock-crooner who demands to know where to find Yum-Yum, the beautiful ward of a tailor named Ko-Ko. Nanki-Poo explains that he met Yum-Yum a year ago while playing second trumpet – an instrument that he plays without much talent – in the Titipu big band ("A Wand'ring Minstrel, I"). It was love at first sight, but hopeless, since she was engaged to her older guardian, Ko-Ko. However, Nanki-Poo has recently heard the happy news that Ko-Ko has been condemned to death by the almighty Mikado for breaking the law against flirting, and has rushed to Titipu in order to marry Yum-Yum.

Nanki-Poo is informed by the extremely cool Pish-Tush and Pooh-Bah that Ko-Ko has since been freed by the people of Titipu and made Lord High Executioner, its highest ranking official. Pooh-Bah, who became Lord High "everything else" after all of the other officials resigned in protest, also offers (for a small fee) the information that Yum-Yum and Ko-Ko are slated for marriage that very day ("And the Drums Will Crash"). Nanki-Poo is determined to find Yum-Yum at all costs before the wedding takes place.

Ko-Ko ceremoniously enters ("Behold the Lord High Executioner"), proclaiming his enthusiasm for ridding society of Ragtime Serenaders, Recluses, Revivalists and any other offenders on his list ("I've Got a Little List"). As Ko-Ko bribes Pooh Bah's multiple official positions into giving him wedding advice, Yum-Yum enters with her two scatting sisters, Peep-Bo and Pitti-Sing ("Three Little Maids"). Ko-Ko tries to kiss his unwilling bride-to-be, when Yum-Yum suddenly collides into Nanki-Poo. The lovestruck trumpet player begs her to turn down Ko-Ko and marry him instead, but Yum-Yum points out that a wandering minstrel is hardly a suitable husband for a ward of the Lord High Executioner. Nanki-Poo confesses to her that he is, in fact, no musician – instead, he is the son of the Mikado, himself! He had been forced to flee for his life to Titipu when Katisha, an older woman in the Mikado's court, claimed him in marriage under the Mikado's flirting law. While Nanki-Poo and Yum-Yum realize that the law prohibits them from ever gazing into each others' eyes and breathing sighs of unutterable love, they still sneak one regretful kiss ("This Is What I'll Never Do").

Ko-Ko, trying in vain to soliliquize, receives a letter from the Mikado stipulating that, unless someone is beheaded within a month, his position will be abolished and Titipu will be reduced to village status. Since Ko-Ko is already under sentence of death for flirting, Pooh-Bah and Pish-Tush suggest that he simply execute himself. Ko-Ko points out that, not only is self-decapitation difficult, but that suicide is a capital offense. He tries to appoint Pooh-Bah as Lord High Substitute, but Pooh-Bah declines the honor ("I Am So Proud"). With no one willing to act as a volunteer, Ko-Ko is left to figure out a solution.

The solution arrives in the person of Nanki-Poo, who, devastated that Ko-Ko is going to marry the girl whom he loves, is searching for a tree in order to hang himself. Nanki-Poo is persuaded by Ko-Ko to be his substitute on the chopping block, but on one condition: that Yum-Yum be his bride until he is beheaded at the end of the month. Ko-Ko begrudgingly consents to the marriage, and there is much rejoicing by all ("Let the Throng Our Joy Advance").

Suddenly, Katisha appears, claiming Nanki-Poo for herself ("Katisha's Entrance"). She is informed by Pitti-Sing and the rest of the company that, unfortunately, her request cannot be fulfilled because of his upcoming wedding. ("For He's Going to Marry Yum-Yum"). Katisha soulfully mourns her lonely fate ("The Hour of Gladness") before spitefully attempting to reveal Nanki-Poo's true identity. Yum-Yum, anticipating her intentions, drowns her out in song. A vengeful Katisha is finally pushed offstage by a celebratory ensemble, which insists that nothing should be permitted to ruin the festivities to come. ("Finale – Act One")

Act Two

The women prepare Yum-Yum for the upcoming wedding behind lowered shades as the men stare at the pretty bride-to-be's silhouette ("Braid the Raven Hair"). Yum-Yum contemplates, in her artless Japanese way, how much more attractive she is than anyone else in the entire world ("The Sun and I"), but her happiness is shattered when she's reminded that her husband is to be beheaded in a month. Nanki-Poo suggests that time is purely arbitrary – if each "second" is called a "minute," they've got thirty years of married happiness before them. As the wedding procession begins, the company unsuccessfully endeavors to look on the bright side of the situation ("Swing a Merry Madrigal").

Before the wedding can take place, Ko-Ko announces his latest discovery: he will not be able to marry Yum-Yum after all, since, according to the Mikado's law, when a married man is beheaded, his wife must be buried alive! Nanki-Poo realizes that, by insisting on the wedding, he dooms Yum-Yum to a hideous death. However, if he releases her from her promise, she must marry Ko-Ko at once ("Here's a Howdy Do")! To Ko-Ko's dismay, Nanki-Poo decides that the only way to solve the problem is to hang himself as he originally planned.

Pooh Bah announces the approach of none other than the Mikado, himself, causing Ko-Ko to insist that Nanki-Poo honor his contract and die by the hands of the Lord High Executioner. To his surprise, Nanki-Poo accepts. Ko-Ko admits that, in truth, he is incapable of killing even a fly – he had always thought his duties as Lord High Executioner were purely nominal. To convince the Mikado that his orders have been followed, Ko-Ko suggests that they create a certificate of Nanki-Poo's execution, witnessed by all of the officials of Titipu (i.e., Pooh-Bah... for some cold hard cash). However, Nanki-Poo must promise to leave and never return. Nanki-Poo agrees to do so only on the condition that he marry Yum-Yum immediately.

The Mikado, a cool cat who believes that the punishment should always fit the crime ("The Mikado Song"), demonstrates how to tap any troubles away. Ko-Ko informs him that the demanded execution has taken place but quickly finds out that the Mikado has come about another matter – his son, who ran away a year ago, has been masquerading in Titipu, disguised as a second trumpet player. Ko-Ko, Pooh-Bah and Pitti-Sing try to convince the Mikado that Nanki-Poo is in Cleveland, but Katisha discovers his name on the execution certificate. The Mikado, understanding that Nanki-Poo's true identity had been kept a secret, regretfully points out that the punishment for killing the Heir Apparent doesn't take this into consideration. It is decided that, after lunch, Ko-Ko, Pitti-Sing and Pooh-Bah will die in boiling oil.

Ko-Ko realizes that Nanki-Poo must be brought back to life immediately. However, Katisha would then insist on the execution of the newlywed Nanki-Poo, causing Yum-Yum to be buried alive. Nanki-Poo suggests the ultimate solution – Ko-Ko must marry Katisha! Ko-Ko is reluctant – even Katisha's famed left shoulder blade can't make up for her plain face – but, when Nanki-Poo insists this is the only way he will "reappear" in Titipu, Ko-Ko sets off to win Katisha's heart.

Katisha wonders why death refuses to come and bring peace to her broken heart ("Alone and Yet Alive") as Ko-Ko springs into action, telling her that he'll die on the spot if she doesn't accept his love. Katisha claims no one has ever died of a broken heart, so Ko-Ko responds with the tragic tale of Tit-Willow, a little bird who wasted away due to blighted affection ("Tit-Willow"). Katisha is touched by the story, and the two realize that they are a perfect couple ("Beauty in the Bellow").

As the Mikado prepares to boil Ko-Ko, Pitti-Sing and Pooh-Bah in oil, Katisha begs him to show them mercy, particularly since she is so koo-koo for Ko-Ko, she has gone and married him. The Mikado is understanding, but mentions that this does not solve the problem – the Heir Apparent is still slain. With that, the Heir Apparent himself appears, along with the Mikado's new daughter-in-law, causing everything to fall happily into place as the Mikado calls the show to an end ("Finale – Act Two").