The alligator was one of the animals from the desert near 3 Stooges Ghost Town.
It is a green alligator.
It seemed to enjoy resting, but when it met Scooby-Doo, it got terrified.
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It was one of the animals that Shaggy Rogers spotted in the desert, along with a camel and an orangutan. When Scooby saw the mechanical T-Rex on the cliff, he quickly dug under the sand and when his head pocked out, he noticed a resting alligator next to him and when the gator woke up, they were both frightened.