"Two for the Zoo" begins by introducing Timon, a meerkat, and his warthog friend, Pumbaa. At the start of the episode, Pumbaa takes a mud bath while Timon chases a beetle. Then the meerkat runs into a buzzard, who soon gets captured by Quint, who puts it in a truck to a zoo. Pumbaa disapproves of that, but Timon tells his friend that it would be great to live in a zoo.
Timon is going to try to get himself and Pumbaa captured by Quint to get to the zoo. Quint puts leaves on a pit, which is a trap. Timon pretends that he wants to nap on the leaves, but Pumbaa quickly rescues his friend, and instead, a lion falls in the pit.
Timon and Pumbaa try another way to get themselves captured, this time using a rope. Timon asks Pumbaa to hold the rope for a second and comes back with toothbrushes. The meerkat sees his friend not holding the rope and the two see that the rope got attached to a rhino's horn. As the rhino goes after Timon and Pumbaa, a crate falls and traps him.
For the third attempt to get themselves captured, Timon and Pumbaa use a big net. When they struggle to trap themselves, Pumbaa asks a gorilla to help them. However, when the gorilla does so, it gets itself captured. Then when coconuts fall on Timon and Pumbaa, a snake lands on the coconuts and Quint captures the snake and thanks Timon and Pumbaa for "helping him capture the animals."
Timon and Pumbaa try one more way to get themselves captured: sneak inside the back of the truck. When the two are about to get in, they see the animals they accidentally help Quint capture in cages angry at them. Timon then changes his mind about getting captured; instead have him and Pumbaa stay in the jungle.
Timon lies on a hammock while Pumbaa lies in a mud. Timon is about to eat a tortilla with bugs inside, but Pumbaa keeps moaning about the animals being behind bars and he wants him and Timon to go free them. When the two get to the zoo, Quint shows up and considers Timon and Pumbaa to be the snake's food. He therefore puts Timon and Pumbaa in a bag and drop to the snake's den so they can get devoured by the reptile.
After Timon and Pumbaa fly out of the snake's tail and land on two hedgehogs, Timon wants to leave the zoo, but Pumbaa moans again and Timon has to find a way to free the animals. The two dress up as cleaners and Quint makes the them get in the gorilla's cage. The gorilla puts Timon and Pumbaa on a tire swing and makes them fly off and land in the rhino's cage. The rhino pokes Timon and Pumbaa with its horn and the two fly off and land on the lion's cage.
After Timon and Pumbaa escape the lion, Pumbaa sees a machine and accidentally pushes a button that opens the cages of the zoo, causing all the animals to escape. Timon and Pumbaa sneak out of the room with the machine and run into the animals they accidentally helped Quint capture.
After the animals attack Timon and Pumbaa, Quint puts the two in their own cage. Pumbaa tells Timon that he was right about living in a zoo. Then it turns out that they're in a petting zoo and they see children on a field trip about to pet them.