After being unfairly accused of committing a crime, Timon and Pumbaa are thrown into jail. In order to clear their names, the two plan a desperate escape into the wild, where they can search for the true criminal.
"Alcatraz Mataz" begins by introducing Timon, a meerkat, and his warthog friend, Pumbaa. At the start of the episode, the two friends are being unfairly arrested and thrown into jail by the Vulture Police. As the cell closes them in, Timon pleas with the guards to recognize their innocence, but the Vulture Police dismiss his words as lies and leave the two to sulk in their cell.
After the police are gone, Timon and Pumbaa are taunted from their jail cell window by Toucan Dan, the crime's true culprit. As the toucan flies away, Timon proclaims to Pumbaa that they must escape in order to establish justice. The two proceed to dig out of their jail cell with spoons. Though the plan at first seems to succeed, the friends are eventually caught and caged once more by an irritated Vulture Police.
In a later attempt, in which Timon and Pumbaa pull the breakout lever, releasing all the prisoners, the two actually manage to escape. While in hiding, Timon angrily laments their predicament, proclaiming that they must find Toucan Dan and force him to admit his involvement in the crime.
After encountering the toucan in his hideout, Timon and Pumbaa try various techniques to make him confess, but he outsmarts them each time. However, when the two stumble upon stolen goods in his footlocker, the Vulture Police arrive on the scene, and Toucan Dan is convicted of his crimes. Timon and Pumbaa aren't free themselves, since they have now escaped jail illegally, and the police proceed to throw them into prison once more. As the vultures turn their backs on the criminals, Timon and Pumbaa exchange sneaky glances and pull out spoons.