Kindly Dr. Helms, Man of Science, is struggling to create new synthetic hormones at Slade Pharmaceutical. Toward this end, valiant Luke Gutchel is supplying him with test animals in the form of dogs kidnapped from the city streets. When kindly Dr. Helms is finished with the test mutts, their hormone-laden carcasses are disposed of in the city's sewers.
The plot is complicated by an event that occurred twelve years earlier, when little Marisa Kendall obtained a baby alligator in Florida, brought it home with her, and named it Ramon. In true urban legend fashion, her father flushes the gator down the toilet, sending it to the sewers where, as it turns out, there's plenty of doggie meat flavored with super growth hormones to chow down on. Ramon grows. And grows. And grows.
After devouring a few people foolish enough to wander into the sewers, Ramon emerges for a jaunt about town, where he's hunted by loathsome police detective David Madison and herpetologist Marisa Kendall. (Yes, that Marisa Kendall; she's grown up now, and determined to kill the alligator she neglected in its infancy. What a bitch.)
From here, the movie becomes a classic morality tale as the forces of Evil (Madison and Kendall) seek to destroy the Good and Pure (handsome and personable, but tragically misunderstood, Ramon).