Three years after being kicked out of the science department for his theory of Time warps, and his attempt on Matt Lauer's life, Rick Marshall is reduced to working as a teacher at the George C. Page Museum until he meets Holly Cantrell whose finding urges him to create a tachyon amplifier to enable time warp travel. They go to the Devils Cave attraction where the finding was found, hiring its tour guide Will Stanton. But once they've activated the tachyon amplifier, losing it in the process, the three end up in a parallel universe where all timelines converge. They soon meet some ape men, Pakuni, two of whom were going to kill the younger one, when Stanton unintentionally gives the other two the secret of fire as they run off. The gang then proceed to help the other one, named Cha-Ka, until he runs off with them in pursuit.

Once catching up to Cha-Ka, they are trapped by a tree which turns out to be a dinosaur feeding site, being attacked by a Tyrannosaurus. The T. rex chases them until they come to a small land bridge. Marshall is convinced they are safe as he explains how a T. rex has a walnut-sized brain, and is incapable of judging depth and distance. Hearing this as he stalks away, the T. rex stops in his tracks, turns, and runs full speed to jump across the chasm. Chasing them until they reach a crevice in a cave, it gives up, though still wanting to eat Marshall. Holly, knowing the dinosaur's attitude, gives him the name "Grumpy". Though Marshall didn't believe it to be possible, Grumpy's vendetta becomes more apparent when he leaves a gify, beach-ball sized walnut, gift-wrapped.

The next day, Cha-Ka brings fruit full of spiders. Rick pours dinosaur urine all over himself as a way to masks his scent from "Grumpy" he then has visions about a strange creature begging for his help, running out into the Lost City. The others follow as Cha-Ka gets agitated and attempts to tell them they should leave as they are attacked by the slow yet deadly Sleestaks. But when the Pylon opens, Marshall and company enter, meeting the creature who contacted them, Enik. Enik tells them that the evil Zarn is out to control the universe and needs the tachyon amplifier.

In spite of Will's feelings, Marshall offers his aid as Cha-Ka takes the group through the jungle and onto a salt flat landscape that is a feeding site for Compsognathus and Velociraptors, who proceed to tear an ice cream man to pieces until Grumpy comes and scares them off. However, a female Allosaurus arrives as well. The two territorial predators prepare to fight when the both of them catch Marshall's urine-drenched scent and chase after him. Though managing to outsmart Grumpy, Marshall runs from "Big Alice", the Allosaurus, until he reaches Holly and Will, using the tank of liquid nitrogen to freeze the Allosaur before she explodes with the tachyon amplifier among her remains. After that, a Pteranodon steals their time machine.

Though down in the dumps, Marshall regains his confidence as he attempts to apologize to his friends in song (The theme song to the original TV series) while unknowingly attacked by a giant mosquito. After managing to get the tachyon amplifier back from a nest of pterosaurs, they return to a motel back in the salt flat. While Marshall, Will and Cha-Ka laze in the pool, Holly goes, finding a Pylon. Inside, she finds dinosaur eggs lodged in dinosaur feces, taking one out before she find a holographic message from the Zarn, learning that Enik is the real villain and being taken by a Sleestak to stand trial for aiding him.

Meanwhile, after eating a Giant Crab, which killed itself by stepping on a geyser while advancing on them, the three realize Holly's missing and go find her. They meet two mating Sleestaks, that shed their skin, which Marshall and Will use to disguise themselves while Cha-Ka goes to get Enik. Arriving to Holly's aid as she is condemned to death by the Library of Skulls, Marshall and Will learn that Enik was the one who wiped out the Altrusians while confirming Will's feelings about the villain's tunic. After saving Holly, the gang confront Enik and his Sleestak slaves, taking the tachyon amplifier while revealing his plans on using the Sleestaks to overpopulate the worlds. He then leaves Marshall and company to their fate as Grumpy arrives to get his revenge.

Seeing no other way, Marshall takes on Grumpy one-on-one, ending with Marshall vaulting into the dinosaur's mouth. Though Holly chides him for it, Grumpy shrugs her off and leaves as she and Will attempt to fight off the numerous Sleestaks. However, after being excreted out while taking out some intestinal trouble, Marshall and a "less grumpy" Grumpy make their peace as they arrive to kill most of the Sleestaks. Entering the Pylon, Marshall and company manage to destroy the crystal shard that powers it, with Will choosing to stay with Cha-Ka in the Land of the Lost while holding Enik off so Marshall and Holly can return home. Will takes advantage of his new life by meeting Cha-Ka's harem which he was told earlier by Cha-Ka that they were ugly only to find them to be very hot Caribbean tanned women wearing only a loincloth. He almost immediately get surrounded by half a dozen women who start rubbing him all over. He responds to this by saying " I made the right choice."

Back on Earth, Matt Lauer reluctantly gives a second interview with Marshall this time proven right and proceeds to rub it in Matt Lauer's face by bringing a dinosaur egg back and giving him a signed copy of his new book. But after being forced to show off the title of Marshall's new book, ''Matt Lauer Can Suck It'', history repeats itself with Matt trying to kill Marshall. Soon after the show ended, unaware of what Marshall and she left behind on the set, the dinosaur egg Holly found hatches into a baby Sleestak