A hapless store clerk must foil criminals to save the life of the man who, miniaturized in a secret experiment, was accidentally injected into him.
Tuck Pendleton is a cocky pilot, who is taking part in a miniaturization experiment. When some bad guys break into the lab to steal the technology, one of the scientists takes a syringe which contains the miniaturized Tuck and vessel. Now in the vessel is part of the material needed to restore him. But the other part which is the lab is stolen. The scientist's shot but before dying he injects Tuck into Jack Putter, a hypochondriac, who feels that something is wrong with him all the time. When Tuck links himself to Jack's systems, he discovers that something happened. So they go back to the lab, and discover what happened. Now they are told that unless they retrieve the material that was stolen they won't be able to restore Tuck before his oxygen is depleted. Now the government rep decides that the only thing that matters that as long as they have the other half of the material, it is useless to the thieves. So Tuck eggs Jack to go out and find the thieves. They enlist the aid of Tuck's old girlfriend, Lydia, who is a reporter. And it's fortunate for them that she has a lead that pans out.
A scientifically miniaturized marine unexpectedly finds himself floating around the body of a hypochondriac, and trying to outwit saboteurs who want the device that shrank him. Attempts by his colleagues to retrieve the little man - protected inside a tiny submersible - are hampered by the would-be thieves.
Lt. Tuck Pendelton, an American pilot, takes part in an experiment where he is miniaturized inside a submarine-like craft and is to be injected into a rabbit. The bad guys try to steal him, and the machine, while he is miniaturized, and eventually he ends up inside Jack Putter, a hypochondriac.
Vector Scope is one of the largest science corporations on the west coast of the U.S. They have chosen Lieutenant Tuck Penelton, who is a free-spirited fighter pilot with no respect for life, for a miniaturization program developed by Vector Scope. However, when group of hired thugs infiltrated Vector Scope, they stole a unique micro chip, making miniaturization possible. Ozzie, a scientist, manages to escape with Tuck, in hand, miniaturized in a syringe. Ozzie makes a last ditch effort to save Tuck's life by injecting him into a person named Jack Putter, an overly paranoid cashier at a local grocery store. What Jack will soon realize that with Tuck floating inside his own body, he will embark on a journey to attempt to recover the chip before it falls into the hands of a technology smuggler, Victor Scrimshaw. He intends to sell the chip to a nameless criminal known as "The Cowboy".
- In San Francisco, California, down-on-his-luck naval aviator Lt. Tuck Pendleton (Dennis Quaid) resigns his commission and volunteers for a secret miniaturization experiment. At a party that opens the story, Jack gets into a fight with several other pilots whom he'd just insulted. He's turned over to his girlfriend, Lydia Maxwell, who takes him to his trashy apartment. Tuck convinces her to spend the night and the two make love. The next morning, Lydia is trying to leave before Jack wakes up and the two argue: Lydia feels Jack drinks too much and is reckless. She finally is able to leave in a cab.
Tuck reports to the labs of Vectrocon, the research company conducting the miniaturization experiment. Through a complex process, Tuck and the craft he will pilot are shrunk to microscopic size and transferred into a syringe to be injected into a laboratory rabbit. Just as Tuck is about to be injected, the lab is attacked by a rival organization led by scientist Dr. Margaret Canker (Fiona Lewis) that plans to seize the experiment and steal the miniaturization technology. Two prototype microchips are necessary: one for miniaturization, the other for re-enlargement. Vectrocon is the first company to master the more difficult re-enlargement process. During the attack in the lab, Canker steals the second microchip.
Experiment supervisor Ozzie Wexler (John Hora), knowing their intentions, escapes with the syringe. A chase ensues with one of Canker's henchmen, the cyborg Mr. Igoe (Vernon Wells), which ends at a nearby shopping mall. Igoe possesses a bionic hand containing a small projectile weapon like a gun and shoots Ozzie. The now-dying doctor injects Tuck and the pod into an unsuspecting Jack Putter (Martin Short), a hypochondriac Safeway grocery clerk, the first person he comes into contact with, dying shortly after. Igoe finds the broken syringe and makes a note of Jack himself.
Tuck falls unconscious during the sudden injection and when he awakes is unaware of what has happened and believes he's been injected into the rabbit. After attempts to radio the lab are unsuccessful, Tuck navigates the pod to the optic nerve and implants a camera so he is able to see what the "host" sees. Realizing he is inside a human, Tuck makes contact by attaching another device to Jack's inner ear, enabling him to talk to Jack, initially with embarrassing consequences. Tuck explains that the pod has only a 24 hour supply of oxygen and needs his help in order to extract him by going back to the lab.
Jack, after an embarrassing incident at his job and after talking to his doctor, goes to the lab to talk to Dr Niles (Mark L. Taylor) and head of security, Pete Blanchard (Harold Sylvester). He has Jack ask what went wrong; security for the experiment failed and that the chips are prototypes. Tuck talks Jack into leaving the lab and finding Lydia whom he thinks can help Jack get the second chip back.
Jack makes contact with Lydia, who's a reporter who has had dealings with a stolen goods dealer, The Cowboy (Robert Picardo). They learn that The Cowboy plans to buy the computer chip from Scrimshaw. After psyching Jack up, Tuck has Jack knock The Cowboy unconscious. Tuck then activates an experimental process that controls the muscles of Jack's face, altering Jack's features so he looks identical to the Cowboy. Lydia and Jack, posing as the Cowboy, meet with Scrimshaw to steal the chip from him. However, just as they're about to take possession of the chip, Jack accidentally tips Scrimshaw and Canker that he's an imposter. Scrimshaw plans to torture Jack by having Igoe burn him with a torch built into his bionic arm. Jack's nervousness overrides the transformation of his face, revealing his true face. Mr. Igoe captures Jack and Lydia and takes them to the lab. While imprisoned, Jack and Lydia share a kiss, which, unknown to them, transfers Tuck into Lydia's body through their saliva. Once taken to the lab, the criminals miniaturize Igoe shrink him in a more sophisticated pod and inject him into Jack to locate Tuck, kill him, and obtain the other chip, which is attached to the pod.
Once Igoe has been injected, Jack and Lydia escape, steal back the chip and order everyone in the lab at gunpoint into the miniaturization device, including Scrimshaw and Canker. However, not knowing how to operate it, they only manage to miniaturize everyone to 50% of the original size. Tuck, now inside Lydia, finds a growing baby and realizes that she is pregnant with his child. By going to Lydia's eardrum and playing their song (Sam Cooke's "Cupid"), he is able to alert them what has happened. Jack and Lydia kiss again to transfer Tuck back. They frantically drive back to the lab in order to enlarge Tuck, not realizing that miniature versions of Scrimshaw and Canker are hiding in the back seat. While the villains attempt to subdue Jack and Lydia, Mr. Igoe locates Tuck in Jack's esophagus and attacks him. Tuck disables Igoe's craft, fighting him off for a few minutes and passes through to Jack's stomach, hanging above a pool of acid. Igoe attacks again, having ejected himself from his armored suit and tries to drill into the cabin of Tuck's pod. Tuck, to make Jack even more nervous, tells his host that he saw what may be a tumorous growth. Jack's ulcer reacts and he produces more stomach acid. When the pool is deep enough, Tuck detaches and plummets with the screaming Igoe attached, dissolving him to his skeleton.
Back at the lab, with only minutes of supplemental oxygen left in the pod, Jack follows Tuck's instructions to eject the pod from his lungs by making himself sneeze. One of the lab scientists finds the pod on Dr Niles' glasses and gently retrieves it. Tuck and the pod are successfully enlarged, and he is reunited with Lydia and finally gets to meet Jack in person.
The film ends at Tuck and Lydia's wedding, held at Wayfarers Chapel, where Tuck wears the chips from the experiment as cufflinks. When they climb into the limousine, it is revealed that Cowboy is the driver and the shrunken down Scrimshaw and Canker are hiding in the trunk, inside a suitcase. Now confident and in control of his life, Jack recognizes the Cowboy. He bids farewell to his doctor, his boss and a woman he'd tried to date, Wendy and jumps into Tuck's vintage 1967 Mustang, pursuing the limousine to rescue the newlyweds.