The film begins with a young girl attending an exciting alligator stunt show during a family vacation in sunny Florida. As the audience marvels at thrilling interactions with the alligators, chaos ensues when one of the performers is unexpectedly attacked and mauled. The spectators react with a mix of shock and fascination, while the show's proprietors seize the moment to sell baby alligators as souvenirs. Captivated, the little girl purchases one, names him Ramon, and takes him back to her home in Chicago, putting him in an aquarium. Unfortunately, her joy is short-lived when her father, in a fit of anger, flushes Ramon down the toilet. However, unbeknownst to them, Ramon survives, making the city's sewer system his new home.
Fast forward 12 years, and we meet David Madison, a Chicago police detective portrayed by Robert Forster. He's struggling to redeem himself following a tragic incident that resulted in his partner's death. A disturbing series of events unfolds as human body parts begin to surface in the city's water filtration systems. Madison, determined to solve the mystery, takes a rookie officer with him into the dangerous depths of the sewer, only to encounter a ferocious adversary: an enormous alligator that appears to be Ramon, who has dramatically grown to a staggering 36 feet. In a harrowing attack, Madison manages to escape while tragically losing his partner, further complicating his professional life.
Desperate for help, Madison seeks the expertise of Marisa Kendall, a zoologist played by Robin Riker. Fatefully, she is also the little girl from the opening sequence, who had a keen fascination with alligators before her pet met its untimely end. Though initially doubtful about the alligator's survival in the sewers, Marisa's skepticism quickly dissipates when another victim goes missing, with photographic evidence revealing the monster lurking beneath the surface.
As Madison investigates, he uncovers a sinister link between the alligator's existence and a pharmaceutical company running dubious experiments involving growth hormones on dogs. In a grim cycle, the company has been disposing of their deceased specimens into the sewer, which provides the alligator with an unnatural food source, allowing it to grow to its monstrous size.
With the alligator becoming increasingly agitated by newfound activity in its domain, it surfaces, wreaking havoc across the city. Although facing severe backlash from the police department, Madison is driven by a thirst for revenge against the creature that disrupted his life. Consequently, the city makes several attempts to eliminate the threat, including employing an arrogant big-game hunter to bring down the beast. However, the plan backfires spectacularly when the alligator ambushes the hunter in a dark alley.
In a dramatic climax, the owner of the pharmaceutical company finds his lavish black-tie event turned upside down as the alligator crashes the party, leading to a chaotic scene where several guests meet grisly ends and the owner himself is killed inside his limousine.
As the tension peaks, Madison and Marisa devise a plan to finally put an end to the alligator's rampage. Madison descends into the sewer armed with a bomb, while Marisa stays above ground to manage his escape route. Just when it seems all hope is lost, Madison narrowly avoids disaster when a woman unwittingly blocks his exit. However, they manage to coordinate their efforts just in time. In an explosive finale, Ramon is obliterated, but viewers are left with a chilling reminder of the cycle continuing, as another baby alligator emerges from a drainpipe in the sewer, hinting at the dangers that lie ahead.
