Act I
Pere Ubu, together with Mere Ubu and Captain Bordure, devise a plan to assassinate the King of Poland. Pere Ubu poisons Bordure’s men at a lavish feast by having them taste an excrement-covered toilet brush. The act concludes with Pere Ubu demanding that Mere Ubu, Captain Bordure, and the other conspirators "swear to kill the king properly."

Act II
Pere Ubu attacks and kills King Venceslas of Poland. Queen Rosemonde and her youngest son, Bougrelas, flee to a mountain cave, where the Queen dies. The spirits of dead ancestors appear to Bougrelas, urging him to seek revenge and bestowing upon him a large sword.

After being prompted by Mere Ubu to share some of his newly acquired wealth, Pere Ubu throws gold coins to the crowd, causing a stampede in which several people are trampled. Pere Ubu responds by offering more gold to the winner of a footrace. Subsequently, Pere Ubu invites everyone to an orgy at the palace.

Act III
Pere Ubu and Mere Ubu discuss their next steps now that they rule Poland. Pere Ubu decides against promoting Captain Bordure to the rank of Duke of Lithuania, deeming him unnecessary. Bordure is imprisoned in Pere Ubu’s dungeon but manages to escape and ally with Czar Alexis. Meanwhile, Pere Ubu executes all the Polish nobles to claim their properties, then does the same with the magistrates and financiers under the guise of reforming the law and financial system. Realizing that all government officials are dead, Ubu nonchalantly decides to collect taxes himself, going door to door.

Bordure sends Ubu a letter revealing his plan to invade Poland and restore Bougrelas as the rightful king. Ubu weeps in fear until Mere Ubu suggests they go to war. Pere Ubu agrees but insists he will not "pay out one sou" for the expenses. With a cardboard cutout of a horse’s head around his neck, Ubu leads his army into battle against Bordure, Czar Alexis, and Bougrelas.

Act IV
Mere Ubu searches the crypt containing the remains of the former Kings of Poland for the hidden treasure. She finds the treasure among the bones but realizes she cannot carry everything at once. When she declares she will return the next day for the rest, a voice from one of the tombs exclaims, "never, Mere Ubu." Bougrelas advances to Warsaw and triumphs in the initial battle. Mere Ubu flees amidst rifle shots and a barrage of stones. Meanwhile, Pere Ubu engages in battle with the czar in Ukraine. The conflict sways back and forth until Pere Ubu and his forces are ultimately defeated. They retreat to a cave in Lithuania. While in the cave with two soldiers, a bear attacks; Ubu climbs to safety on a rock, and when asked for help, he mutters a Pater Noster ("Our Father, who art in heaven..."). After the soldiers kill the bear, Ubu falls asleep, and the two soldiers decide to seize the chance to escape.

Act V
After a four-day journey across Poland to evade Bougrelas and his army, Mere Ubu reaches the cave where Pere Ubu is restlessly sleeping. Unnoticed by her husband, Mere Ubu pretends to be a supernatural entity to compel Pere Ubu to seek forgiveness for his "bit of pilfering." Instead, Pere Ubu delivers a litany of her flaws. Realizing it is Mere Ubu in the cave, Pere Ubu throws the dead bear on top of her. Fearing it might still be alive, Pere Ubu climbs onto the rock and starts the Pater Noster routine again. Infuriated by Mere Ubu's laughter, Pere Ubu begins to tear her apart. However, before he can inflict much harm, Bougrelas and his army arrive, decisively defeating the Ubus, who barely manage to escape to a ship on the Baltic Sea. Pere Ubu plans to get himself appointed Minister of Finances in Paris, aiming to restart the entire sordid series of events.