Plot

In San Francisco, down-on-his-luck naval aviator Lt. Tuck Pendleton (Dennis Quaid) resigns his commission (He is a Bona Fide hero but is frustrated that he never got his due recognition from the air force and was always passed over for the meaty assignments. All this culminated in a drunken escapade at an official reception, where Tuck embarrassed himself and his girlfriend Lydia, who vows never to see him again). Tuck volunteers for a secret miniaturization experiment. 2 months later, He is placed in a submersible pod, and both are shrunk to microscopic size. The procedure requires 2 chips (one embedded in the pod, other in the control panel), one is required for miniaturization, but both are required for re-enlargement). They are transferred into a syringe to be injected into a rabbit, but 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 (Along with the chip that was in the control panel).

Experiment supervisor Ozzie Wexler (John Hora), knowing their intentions, escapes with the syringe. A chase ensues with one of Canker's henchmen, Mr. Igoe (Vernon Wells), which ends at a nearby shopping mall. After being shot, Ozzie 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. Jack's doctor has told him that he needs rest and relaxation and the last thing he needs in his life is excitement.

On regaining consciousness, Tuck is unaware of what has happened and believes he has been injected into the rabbit. After attempts to radio the lab are unsuccessful, he 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, he makes contact by attaching another device to Jack's inner ear, enabling him to talk to Jack. Meanwhile Jack rushes to his doctor as he thinks he is possessed and can hear voices from inside of him. The doctor sends Jack home to rest. At home, Tuck again establishes contact with Jack and explains to him about the experiment. Jack explains that the pod has only a few hours' supply of oxygen and needs his help in order to extract him by going back to the lab. Jack is attacked by Igoe's men, but Tuck instructs Jack in combat and helps him escape.

At the lab, Jack and Tuck overhear the conversations and learn that a) Tuck can't open the hatch as change in cabin pressure will kill him. b) his air supply will run out by 9 am the next day c) The 2nd chip required for re-enlargement was stolen and there are no duplicates The military liaisons suggests letting Tuck die and just work on developing a duplicate chip to salvage the pod. Tuck knows that he is on his own. The rival mastermind is Victor Scrimshaw (Kevin McCarthy). His henchmen include Canker, Igoe, and "The Cowboy" (Robert Picardo).

Jack contacts Tuck's estranged girlfriend, Lydia Maxwell (Meg Ryan), a reporter who has had dealings with The Cowboy (A tech dealer, who is in the market for the stolen miniaturization tech). Lydia has trouble believing Jack but agrees to help him. Jack is abducted by Igoe and Lydia helps rescue him. Lydia learns that the cowboy is in town and speculates that he plans to buy the computer chip from Scrimshaw. After locating and knocking him unconscious, Tuck uses the pod's equipment to control Jack's face muscles, altering his features so he looks like The Cowboy. Lydia can't believe this either, but somehow Jack convinces her that its him. Lydia and Jack, posing as The Cowboy, meet with Scrimshaw to steal the chip from him. However, as they are about to take possession of it, Jack's nervousness overrides the transformation of his face, exposing the scam.

Igoe captures him and Lydia and takes them to their laboratory. While imprisoned, Jack and Lydia share a kiss (after Jack tells Lydia that tuck is inside of him and tells her a really personal story that only Tuck knew about her. Lydia thinks that Jack is Tuck), which, unknown to them, transfers Tuck into Lydia's body through their saliva. Once taken to the laboratory, the criminals shrink Igoe and inject him into Jack to locate Tuck, kill him, and obtain the other chip that is attached to the pod.

Once Igoe has been injected, Jack and Lydia escape, steal back the 2nd chip, and order everyone, including Scrimshaw and Canker, in the laboratory at gunpoint into the miniaturization device. However, not knowing how to operate it, they only manage to shrink everyone to half the original size. Tuck, now inside Lydia, finds a growing baby and realizes that she is pregnant with his child. By going to her eardrum and playing their song (Sam Cooke's "Cupid"), he is able to alert Lydia what has happened. Jack and Lydia kiss again to transfer him back. They frantically drive back to the lab in order to enlarge him, not realizing that the shrunken Scrimshaw and Canker are hiding in the back seat. While they attempt to subdue Jack and Lydia, Igoe locates Tuck in Jack's esophagus and attacks him. Tuck disables Igoe's craft, and he is killed after Tuck drops him into Jack's stomach.

Back at the lab, with only minutes of supplemental oxygen left in the pod, Jack follows Tuck's instructions to eject it from his lungs by making himself sneeze due to his hairspray allergy. 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 cuff-links. When they climb into the limousine, it is revealed that The Cowboy is the driver, and the shrunken Scrimshaw and Canker are hiding inside a suitcase in the trunk. Now confident and in control of his life, Jack recognizes The Cowboy and jumps into Tuck's vintage 1967 Mustang, pursuing the limousine to rescue the newlyweds.