Because of Timon's rudeness, he and Pumbaa get kicked off a cruise ship, and they sail to a deserted island. There they are greeted by a mad scientist who wants to clone Timon.
"Mook Island" begins by introducing Timon, a meerkat, and his warthog friend, Pumbaa. At the start of the episode, a cruise ship leaves while Timon and Pumbaa are on a lifeboat, with Pumbaa telling the crew to come back, showing that they have apparently been thrown out. Pumbaa gets mad at Timon for being rude to the people by calling them a "mook." The two then see a tropical island and get on it, but Pumbaa tells Timon that the island gives him the creeps.
Timon and Pumbaa run into meerkat clones that look just like Timon, but are grey and huge. The clones kidnap Timon and Pumbaa and take them to a laboratory where they meet a mad scientist named Dr. Screwloose, who tells them that the Timon clones are called Mooks. Pumbaa tries to figure out what the clones remind him of until he remembers that years ago, he and Timon were at a restaurant in Paris, France. In the flashback, a waiter gives Timon a Cordon Bleu, but Timon throws it away because he asked for Bug Jubilee and starts being rude to the waiter. According to Pumbaa, the waiters asked Timon to become one of them because of his rudeness. Then a man (Dr. Screwloose from years ago) shows up and pulls out a piece of Timon's DNA and runs off.
Back to the present, Screwloose explains that he used Timon's hair to create and entire race of really rude beings, making Pumbaa finally realize that the clones are of Timon. The warthog then wonders why Screwloose wants to clone Timon create a race of rude beings, which makes the scientist tell Timon and Pumbaa about his first date with a girl named Tiffany Taft when he was a teenager, telling them that it went wrong when he was being rude to their waitress, leading to Tiffany to break up with him. He explains to the duo that he created the Mooks so that he can look more polite in comparison to them. Screwloose claims that his experiment did not go well, saying that he didn't take enough genetic experiment from Timon back in Paris and is planning on cloning the meerkat to create a race of Supermooks.
Timon confronts Screwloose by telling him that he won't let him use his gene to treat people rudely. He frees himself from his trap and tries to escape the lab, but Dr. Screwloose sends the Mooks to go after the meerkat. Timon sees his clones following him and cannot escape them. He convinces them that he is their father and that they should do what he says. He makes the Mooks free Pumbaa from his trap, which makes the warthog impressed by his niceness. But then Timon calls his clones "dumb mooks", which makes the Mooks angry and Pumbaa is impressed with Timon's kindness, but Timon then makes the clones angry throw Timon and Pumbaa to the wall. Timon and Pumbaa then escape the laboratory with Screwloose and the Mooks chasing them.
When Timon and Pumbaa get on the lifeboat and leave Mook Island, Screwloose decides to start being nice to other people. He then runs off to have breakfast with Tiffany. Meanwhile, Pumbaa ask Timon if he has ever heard the term, "If you can't say anything nice, don't say anything at all." Timon says he hasn't and says that the guy who said it is a real mook.