Set in a projected 1995, Fantastic Voyage depicts a world where the Cold War has extended into the microscopic realm. The story centers on the Combined Miniature Deterrent Forces (CMDF), a secret military installation capable of shrinking matter. When a defecting scientist harboring the secret to indefinite miniaturization is injured by an assassin's plot, a team is shrunken inside the Proteus submarine and injected into his body to perform a life-saving intracranial surgery from the inside.

The film’s technological dynamic is defined by the miniaturization limit—a sixty-minute window before subjects return to normal size, creating a high-stakes race against biological defense systems. While the film is set on Earth, the vast majority of the action takes place within the "inner space" of the human body, treated as a frontier as mysterious and dangerous as deep space. The world outside is characterized by high-security military complexes and advanced medical diagnostic tools like EEGs and X-rays, which were state-of-the-art concepts at the time of production.

The film is widely cited as a cultural precursor to nanomedicine and targeted drug delivery. While the physical shrinking of humans remains scientifically implausible, the film correctly anticipated the use of lasers in delicate surgery and the development of nanoparticles designed to navigate the bloodstream to treat localized issues like blood clots or tumors. Modern researchers frequently reference the film when discussing the evolution of smart drugs and the ability to manipulate matter at the molecular level, which became a reality in the decades following the film's fictional 1995 setting.