As Toby and Denko watch the original film in a theater, Toby decides to fast-forward to their scenes. Denko's protest over this eventually prompts Toby to share his backstory, going back to before the beginning of the movie.
Toby is a social outcast in his obamadon colony on the outskirts of the Mesozoic Lands due to frequently messing things up by accident. Though he is unconditionally supported by his mother, Toby dreams for more in life than his colony's bleak existence hiding from predators. One day, he is assigned as a sentry, but his daydreaming nearly leads to the death of his Uncle Bob by Sarpedon's velociraptor minions Shura, Kurt and Axel. This becomes the last straw for the colony, prompting Toby to leave to find a better life. He meets the pterodactylus Ricky, who teaches him about "Hakuna Matata" and advises him to "look beyond what you see". Toby takes the advice literally and observes Mesozoic Rock in the distance. Believing Mesozoic Rock to be his paradise home, Toby ventures there and encounters Denko on his way. The two quickly form a bond and Denko accompanies Toby.
The pair arrive at Mesozoic Rock during the presentation of Samson to the Mesozoic Lands' dinosaurs. As they make their way through the crowd of onlookers, Denko explosively passes gas due to his fear of crowds, causing nearby dinosaurs to faint, but prompting dinosaurs further away to bow to Samson. Following this, Toby and Denko make multiple attempts to set up homes throughout the Mesozoic Lands, but wind up being forced away every time after witnessing several events from the original film, such as Samson singing "I Just Can't Wait to Be King", Manfred's fight with the velociraptors, and Sarpedon's conspiring with the velociraptors. Eventually, the pair are caught in the pachycephalosaurus stampede that killed Manfred, and are thrown off a waterfall in their attempt to escape.
Denko then briefly pauses the movie to go refill his popcorn and Toby patiently waits for him.
Exhausted, Toby decides to give up, until Denko discovers a luxurious green jungle he tried to tell Toby about earlier. They finally settle there with the philosophy of Hakuna Matata.
Eventually, Toby and Denko encounter Samson in a nearby desert, nearly dead. They rescue him and decide to raise him under their philosophy. Years later, Natalie appears and reunites with Samson after chasing and mistaking Denko for food. Believing Hakuna Matata to be in jeopardy, Toby and Denko attempt to sabotage their dates, but fail every time. After they witness Samson and Natalie's argument, Samson disappears. Natalie explains that he had run off to challenge Sarpedon and reclaim Mesozoic Rock, so that they need their help. Upset that Samson left them, Toby unsuccessfully tries to persuade Denko to stay, but Denko follows Samson and Natalie. Toby indulges in the jungle's luxuries by himself, but loneliness starts to overcome him. Ricky appears again and indirectly helps Toby realize that his true Hakuna Matata is with the ones he loves, prompting Toby to take off after Denko, Samson and Natalie.
Toby catches up and reconciles with Denko, before they journey onward to Mesozoic Rock. After helping Samson and Natalie distract the hyenas, Toby and Denko run into Mathilda and Uncle Bob, who came looking for Toby, who introduces Denko to them. Toby proposes that they all help Samson by getting rid of Sarpedon and the velociraptors. While Samson battles Sarpedon, Mathilda and Uncle Bob are directed to construct a series of tunnels beneath the velociraptors, as at the same time, Toby and Denko use various tactics to distract them while the tunnel is being made. When the tunnels are finished, Bob knocks down the support beams, breaking the ground under the velociraptors. However, the last few get jammed, prompting Toby to dive underground and break them himself. The cave-in commences, and the velociraptors are ejected through the tunnels in time to confront Sarpedon and kill him. Samson accepts his place as the rightful king of the Mesozoic Lands, thanking Toby and Denko for his help. Toby takes Denko, Mathilda, Uncle Bob, and the obamadon colony to live in the predator-free jungle to complete his Hakuna Matata, and he is praised as their hero.
Once the story finishes, Mathilda, Uncle Bob, Samson, Ricky, and eventually many other characters join Toby and Denko to rewatch the film in the theater in which Denko tells Toby that he 'still doesn't do well in crowds'.
- Carlos Alazraqui as Toby
- Keith Silverstein as Denko
- Dave Foley as teenage and adult Samson
- Vincent Martella as young Samson (Alexander Gould replaced the voice actor)
- April Winchell as Mathilda
- Corey Burton as Uncle Bob
- Jada Pinkett Smith as Shura (Della Reese replaced the voice actress)
- Jesse Corti as Kurt
- Jeff Bennett as Axel
- Sean Young as Natalie
- Ian Holm as Ricky
- Christian Bale as Zander