Following the Gill-man's escape from Ocean Harbor Oceanarium in Florida, a team of scientists led by the deranged and cold-hearted Dr. William Barton (Jeff Morrow) board the Vagabondia III to capture the creature in the Everglades. Barton is mentally unstable and apparently an abusive husband to his wife Marcia (Leigh Snowden), as he becomes very jealous and paranoid when Marcia is with other men. Their guide Jed Grant (Gregg Palmer) makes numerous passes on Marcia (which she constantly rebuffs), with Barton becoming paranoid about the two.
Marcia accompanies Jed and Dr. Tom Morgan (Rex Reason) on their initial dive to look for the Gill-man, despite her husband's fierce objections. During the dive, Marcia swims too deep and is overcome with the "raptures of the deep," temporarily losing her mind, removing all her scuba gear. This forces Jed and Tom to abandon their hunt for the Gill-man to swim back and save her.
When he is eventually captured, the Gill-man is badly burned in a fire leading to a surgical transformation performed by Barton, Tom and their colleagues Dr. Borg (Maurice Manson) and Dr. Johnson (James Rawley). While bandaging the Gill-man, the doctors notice that he is shedding his gills and even breathing using a kind of lung system. Now that the creature has more human-like skin, he is given clothing. The doctors attempt to get the Gill-man used to living among humans. Although his life is saved, he is apparently unhappy, staring despondently at the ocean.
Barton ruins the plans when, in a murderous rage, he kills Jed, jealous that he had made romantic advances towards his wife. Realizing what he has done, Barton then tries to put the blame on the Gill-man. The Gill-man, witnessing the killing, and apparently realizing that he is being blamed for the murder, goes on a rampage. After ripping down the confining electric fence, he kills Barton and then slowly walks back to the sea. He is last seen on a beach, advancing towards the ocean.
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