Tuck Pendleton (Dennis Quaid) is an airforce pilot. His girlfriend, Lydia (Meg Ryan), leaves him because of his drinking problem. Tuck becomes involved in a top-secret project to miniaturize humans and inject them into the human body. Tuck is the first experimental subject; he is to travel, in a tiny pod, inside the body of a lab rabbit.

This is complicated when, once Tuck and his pod have been shrunk and placed in a syringe ready for injection, the film’s villains, led by the sinister Victor Scrimshaw, break into the laboratory and steal the microchip needed to restore Tuck to his normal size. A scientist escapes with the syringe containing Tuck. Iago, Scrimshaw’s henchman, chases him and, to keep the technology out of their hands, the scientist injects Tuck into Jack Tupper (Martin Short), who just happens to be nearby.

Jack is a hypochondriac who works at a supermarket checkout. When Tuck creates a computer link-up to Jack’s vision and hearing, and speaks to him, Jack believes he has been possessed; his physician suspects a psychiatric disorder. After much anxiety, Tuck explains things, enlisting Jack to track down the villains and get the stolen microchip from them. With Lydia’s help, they thwart the villains (and reduce them to half their normal size).

After journeying inside both Jack and Lydia’s bodies (he moves from one to the other when Jack kisses Lydia), Tuck is rescued and restored to his normal size. Tuck and Lydia reconcile and marry, and Jack, given new confidence by having Tuck within him (like a macho kind of internal inspirational tape), is cured of his hypochondria and anxiety and finds a new life for himself.