The film is told through the perspectives of Timon and Pumbaa who watch their side of The Lion King in a cinema, occasionally stopping the footage to talk with one another. Timon shows Pumbaa his backstory, revealing him to be an outcast in his meerkat colony on the outskirts of the Pridelands. While supported by his mother Ma, Timon wished for more in life and left the colony after his Uncle Max is nearly eaten by hyenas Shenzi, Banzai and Ed. He meets mandrill Rafiki who advises him to find his place in the world via Hakuna Matata. Timon wanders into some long grass upon deciding to venture to Pride Rock, meeting Pumbaa for the first time and they become friends very quickly.
The pair arrive at Pride Rock during Simba's presentation to the Pridelands' animals. However, Pumbaa informs Timon that he gets anxious in crowds and passes gas explosively that knocks some of the animals out, making the rest of them kneel. Timon and Pumbaa look for several other places to live, intercepting with other events in the film. They are eventually caught in the wildebeest stampede that takes the life of Mufasa, but survive, and find a vast jungle which they decide to make their home, Timon learning of Pumbaa's own philosophy of Hakuna Matata, embracing it to his fullest. However, the two find Simba and raise him as their own despite the negative effects of Hakuna Matata.
Years on, Nala appears after chasing Pumbaa and reunites with the adult Simba. Timon and Pumbaa attempt to prevent the two lions from getting together, but ultimately fail in their plan. Timon spots Simba running away after his off-screen argument with Nala and laughs it off, Pumbaa feeling guilty. Later, Nala appears asking where Simba is, but Rafiki explains Simba has run off to challenge Scar. Nala goes to follow Simba, whilst Pumbaa argues with Timon, who selfishly declares he has everything he wanted in the jungle but Pumbaa leaves. Rafiki appears to Timon and reminds him that his Hakuna Matata is not a home but friendship, prompting Timon to go after his friends.
At Pride Rock, Timon and Pumbaa evade the hyenas but run into Ma and Uncle Max who came looking for Timon. Whilst Simba fights Scar, Timon, Pumbaa and the other meerkats set a series of tunnel traps that force the hyenas off Pride Rock, just as Simba kicks Scar off the rock to his future demise at the hands of the hyenas. Simba accepts his place as king of the Pridelands, thanking Timon and Pumbaa for helping him. Timon takes Ma, Uncle Max and the meerkat colony to live in the jungle, realizing his true Hakuna Matata is family. At the end of the film, an army of silhouetted Disney characters join Timon and Pumbaa to re-watch the film in the cinema, but Pumbaa informs Timon he still grows anxious in crowds.