In the pilot episode, Stingray is attacked by Titan's forces and Troy and Phones are captured. They are rescued by Titan's slave girl Marina (modelled on Brigitte Bardot), a beautiful mute young woman who can breathe underwater. Troy is immediately smitten with Marina, and Atlanta becomes jealous. Meanwhile Titan swears revenge for Marina's betrayal. Marina becomes a regular member of Stingray's crew, and later acquires a seal pup called Oink, who features in a number of episodes.
Many subsequent episodes involve Titan's schemes to destroy Stingray and Marineville. These often fail due to the incompetence of Titan's spy, Surface Agent X-2-Zero whose voice is modelled on Peter Lorre.
Almost all the characters, places and vehicles in the series have names connected, in some fashion, with the sea. Character names of this type include Captain Tempest (as in storm), Commander Shore (as in seashore), Lieutenant Fisher, Atlanta (from Atlantic), Marina (from marine), and the hostile Aquaphibians. Place names associated with the sea or water include Marineville and Aquatraz; and vehicle names include of course the super-sub, Stingray, itself (named after a type of marine creature), and Titan's deadly Terror Fish submersibles.
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