In 1968, a teenage girl purchases a baby American alligator while on vacation with her family at a tourist trap in Florida. After the family returns home to Chicago, the girl's surly, animal-phobic father promptly flushes the alligator, whom the girl had named Ramón, down the family's toilet and into the city's sewers.
Twelve years later in 1980, the alligator survives by feeding on covertly discarded pet carcasses. These animals had been used as test subjects for an experimental growth formula intended to increase agricultural livestock meat production. However, the project was abandoned because the formula unintentionally massively increased the animal's metabolism, causing it to develop an insatiable appetite. During the years, the baby alligator accumulated concentrated amounts of this formula from feeding on these carcasses, causing it to mutate, growing into a 36 foot (11 m) monster resembling a Deinosuchus-Purussaurus hybrid, as well as having an almost-impenetrable hide.
The alligator begins ambushing and devouring sewer workers it encounters in the sewer, and the resulting flow of body parts draws in world-weary police officer David Madison (Robert Forster) who, after a horribly botched case in St. Louis, has gained a reputation for being lethally unlucky for his assigned partners. As David works on this new case, his boss Chief Clark (Michael Gazzo) introduces him to reptiles expert Marisa Kendall (Robin Riker), the woman who, as a teenager, bought the alligator years earlier, unaware that this alligator is her former pet. The two of them edge into a prickly romantic relationship, and during a visit to Marisa's house, David bonds with her motor-mouthed mother.
David's reputation as a partner-killer is confirmed when the alligator snags a young cop, Kelly (Perry Lang), who accompanies David into the sewer searching for clues. No one believes David's story, due to a lack of a body, and partly because of Slade (Dean Jagger), the influential local tycoon who sponsored the illegal growth experiments and therefore wants the truth concealed. This changes when obnoxious tabloid reporter Thomas Kemp (Bart Braverman), one of the banes of David's existence, goes snooping in the sewers and supplies graphic and indisputable photographic evidence of the beast while sacrificing his own life. The story quickly garners public attention, and a citywide hunt for the monster is called for.
After the police unsuccessfully attempt to flush out the alligator, David is put on suspension. The alligator escapes from the sewers and comes to the surface, first killing a police officer and later a young boy who, during a party, is tossed into a swimming pool in which the alligator is residing.
The ensuing hunt continues, including the hiring of pompous big-game hunter Colonel Brock (Henry Silva) to track the animal. Once again, the effort fails: Brock is killed, the police trip over each other confusedly, and the alligator goes on a rampage through a high-society wedding party hosted at Slade's mansion; among its victims are Slade himself, the Mayor (Jack Carter), and Slade's chief scientist for the hormone experiments and intended son-in-law. Marisa and David finally lure the alligator into the sewers before setting off explosives on the alligator, killing it. As David and Marisa walk away from the explosion, a drain in the sewer spits out another baby alligator that is unseen by anyone, thus potentially repeating the cycle all over again.
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