DeepStar Six is an experimental deep sea United States Navy facility, crewed by a mix of 11 military and civilians, now in the final week of their tour. The project is headed by John Van Gelder (Marius Weyers), in order to test underwater colonization methods, while overseeing the installation of a new nuclear missile storage platform. Already nearing his deadline, Van Gelder's plans are threatened when geologist Burciaga (Elya Baskin) discovers a massive cavern system under the site. Van Gelder orders the use of depth charges to collapse the cavern, to the dismay of Dr. Scarpelli (Nia Peeples), who want to study the potentially primordial ecosystem inside.