Clayton has finished his Skybax training when his friends Hyla, a human female, and Krekor, a Hadrosaur, inform him of a threat to Dinotopia . A band of pirates are stealing and hiding Tyrannosaurus eggs all over the island, attempting to draw the creatures from their nesting grounds so they can search for an artifact of some sort. Clayton is given a Sunstone Prod, a device similar to a staff, to use against the pirates as he hunts for the eggs.
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- Waterfall City The first level is set in Waterfall City. Clayton will have to navigate the canals and streets of the city in search of eggs.
The final challenge involves Clayton jumping on various boats indicated by arrows while a Brachiosaurus swims underneath and raises the indicated boat with its head, allowing Clayton to jump and grab a map revelaing the locations of more hidden eggs. If clayton does not move quickly enough, the waves caused by the dinosaur will hurt him, or knock him into the water and defeats him.
- Treetown The second level is set in Treetown. Clayton will have to climb tree-structures and rely on dinosaur-help to cross the trees.
The final challenge is when Clayton is forced to battle a mechanized Brachiosaurus on tree platforms.
The third level is set in Canyon City. On the back of his trusty Skybax Stratus, Clayton must fly over the canyons and attempt to hit pirates with rocks. This is the only level where he does not officially search for eggs, though after completing this level Hyla mentions that more eggs have been returned.
The final challenge is when Clayton and Stratus must attack and disable a Sky Galley , an aircraft that resembles a primitive blimp.
The fourth level takes place in underwater caverns. Clayton must pilot the Remora, a submarine, clawing through rocks and avoiding sea-creatures in search of eggs.
The final challenge involves the combat with a giant Dunkleosteus. The beast releases smaller fish from its mouth to attack the submersible. The creature can be defeated by positioning the Remora under a hole in the cavern where barrels fall, bouncing several barrels onto the beast and defeat it.
- Diamond Caverns
The fifth and final level takes place in Dinotopia's Diamond Caverns. The terrain is too difficult to go on foot, so Clayton must ride on Kreekor. The two jump about the caverns and locate eggs. Kreekor can headbut any enemies encountered.
The final challenge reveals that there are two halves of the Time Stone. Clayton discovers one half and Lee Crabb , the villain from the Dinotopia book series, arrives with his half and claims to be behind the whole matter. In a Tyrannosaurus strutter, a dinosaur-like machine, Crabb swoops down and attempts to bomb Clayton, as well as hit him head on while running back and forth. Clayton must fight alone without Kreekor and disable the strutter with his Sunstone Prod.
After Crabb is defeated, Clayton takes both halves and gives one to Hyla for safe keeping. The Tyrannosaurs are grateful for the recovery of their eggs and the pirate threat has been eliminated.