While vacationing in Florida, Mr and Mrs Kendall and their 12-year-old daughter Marisa purchase a 10 inch long baby alligator. Upon their return home, the infant alligator proves to be a nuisance and Mr Kendall flushes it down the toilet. It survives the journey through twisting pipes and emerges deep in the sewer system. Unknown to the public, secret hormone experiments are being conducted on dogs, and the dogs are disposed of by throwing their hormone filled corpses into the sewers inhabited by the now growing alligator. After twelve years of feeding on infected dogs, the hormonal chemistry of the alligator is affected and he grows to become a 36 foot long giant. After a series of harrowing experiences, the alligator is forced to break out of the sewer and smash onto the streets.
The Mutation finds a giant alligator on the loose, this time terrorizing some lakeshore property coveted by unscrupulous developer Vincent Brown. Brown's been pumping toxic waste into the sewers that feed into the lake, and the resulting mutation starts to munch on the locals. Investigating the carnage is cop David Hodges, who finds evidence that the malefactor is big and green.