"Pig-Malion" begins by introducing Timon, a meerkat, and his warthog friend Pumbaa. At the start of the episode, Pumbaa fails to catch a bee, so Timon builds a machine that catches bugs. Timon's machine, however, doesn't work. Then, a hedgehog professor named Dr. Tobias J. Exceter shows up, mocks Timon's intelligence, and builds another machine that catches bugs. The machine works.
Pumbaa suggests that he and Timon study to be smart, but Timon refuses to do so. Exceter says that Timon is afraid to learn, and in answer to the hedgehog's mockery, Timon makes him give him some assignments to do. Exceter then gives Timon and Pumbaa homework. At night, Pumbaa does his homework, but Timon is eating pizza and playing with his yo-yo.
The next day, Timon and Pumbaa are at Exceter's university. Pumbaa does his assignments while Timon does nothing except throw paper planes and spitballs at Pumbaa. Exceter calls Timon up and makes the meerkat read what he has. Timon says that the assignment is about boots. Exceter makes him sit down and makes Pumbaa read what he has written. The hedgehog is impressed with Pumbaa's work and puts a dunce cap on Timon.
The next day, Exceter teaches Timon and Pumbaa dance lessons. Pumbaa succeeds and Timon doesn't when he does the disco dance and the disco ball falls on Exceter. Timon gets another dunce cap.
The next day, Timon and Pumbaa are having their final exam on chemistry. Pumbaa passes, but Timon fails and Exceter expels the meerkat. After a depressed Timon leaves, Exceter tells Pumbaa that because of his achievements, he will him an academic position. It turns out that the position he's giving Pumbaa is putting him in a cage and send him to the "Dissection Labs of Hedgehog University," where he and his "large brain" will be used as an experimental test subject. Pumbaa realizes that Exceter tricked him and screams for Timon's help.
Pumbaa and Exceter are now at Exceter's laboratory. The hedgehog prepares to dissect Pumbaa, but Timon shows up, shocks Exceter, and gets Pumbaa out of the cage.
Timon and Pumbaa get in a control room, which Pumbaa calls a dead end. Timon tells Pumbaa that he did his homework and knows the way out. Exceter walks in and warns Timon about an atomic generator. The meerkat fixes it, thinking that it will either transform into a jet car and send him and his friend back to their jungle safely or it will blow the entire university up. He pushes a button on the machine and the whole building explodes. Timon tells Pumbaa that from now on, he will always do his homework, right after he finishes his yo-yo practice.