"Pirates of Pumbzance" begins by introducing Timon, a meerkat, and his warthog friend, Pumbaa.
At the start of the episode, Timon and Pumbaa are applying for a job, but the employment office lady tells them that there aren't many job openings for gassiest bug-eating jungle animals. When she asked them what type of jobs they are seeking, Pumbaa tells her that he always wanted to be a pirate, which Timon replies to his friend that they don't give such jobs. The lady shows them that they actually do give jobs as pirates, much to Pumbaa's excitement. At first, Timon refuses to become a pirate, but reluctantly changes his mind as Pumbaa starts to sob. The meerkat soon says that he will regret that decision.
Timon and Pumbaa are now at a pirate ship, with Pumbaa working as one of the pirate crew while Timon works as the captain's parrot. Captain Bloodbeard, the captain of the ship, orders his crew to get back to work. When he makes Timon force the pirates to work as well, he gives him a bug as a reward, making the meerkat begin to like his job. Bloodbeard then throws all the pirates overboard for what they did.
With Timon and Pumbaa being the only ones left, Bloodbeard makes Pumbaa raise the pirate flag, which the warthog does after replacing the skull on the flag with a smiley face. Angered by what Pumbaa did to the flag, Bloodbeard is about to throw the warthog off the ship until Timon makes him notice another ship with three elderly women and a treasure. The captain suggests that they should steal the old lady's treasure, which Pumbaa finds wrong and realizes that being a pirate wasn't a good idea of a job. He plans to stop Bloodbeard from stealing the treasure.
When Bloodbeard orders Pumbaa to move the ship closer to the women's ship, the warthog purposely fails to do so, making the captain about to throw him overboard once again until Timon tells him that according to the Big Book of Pirate Law, a warthog tricking the pirate by missing an enemy ship is only punishable by death and months containing the letter Q. Following the book of pirate law, Bloodbeard decides not to throw Pumbaa overboard.
Bloodbeard makes Pumbaa fire bombs at the old ladies' ship, but Pumbaa disobeys the captain by firing bombs at the pirate ship, which, according to the book, is the captain's responsibility to plug in the holes created by the bombs. Bloodbeard then has enough of Timon and Pumbaa disobeying his orders and plans on making them walk the plank. Timon and Pumbaa then try to avoid the captain while he's giving chase. When Bloodbeard eventually captures the duo, he makes them walk the plank. But then, Timon and Pumbaa are rescued by the elderly women from the other ship, who turn out to be pirates themselves with the leader being Captain Granny, the toughest little old lady in the Seven Seas.
After stopping Captain Bloodbeard from making Timon and Pumbaa walk the plank, Captain Granny offers the duo jobs as her pets while Bloodbeard works as her parrot.