Viewers enter the Imagination Institute's theater for the Inventor of the Year Award Ceremony, in which professor Wayne Szalinski is receiving the award. Attendees are asked to don their "safety goggles" in preparation for the scientific demonstrations. The show opens with the crew of the show searching for Wayne, when he suddenly flies on stage miniaturized and in a transportation device called a Hoverpod.
He accidentally drops the control box and sends the machine flying off behind the stage out of control. The Hoverpod comes back and shorts out the neon Imagination Institute "Inventor of the Year Award" sign over the audience (at first only some letters are knocked out, leaving "NERD" spelled diagonally).
Wayne's son Nick demonstrates some of his father's other inventions to kill time while the crew searches for him. Wayne's youngest son, Adam, puts a mouse in his father's copy machine and they quickly multiply (in an animation designed by Curious Pictures). This does not go smoothly, and the audience ends up screaming with the loose mice running under their seats and a holographic "Holo-Pet" cat (which transforms into a lion) in their faces used to scare the mice away (designed by Kleiser-Walczak). While the demonstrations go awry, Wayne manages to use his shrinking machine to return himself back to normal size. He brings out the machine to demonstrate its uses by shrinking a family's luggage, saving space and money when traveling.
Unfortunately, the machine goes out of control and shrinks the audience (plus Nick, who pushes Dr. Channing out of the way of the machine's electrobeam). Wayne inspects Nick and the audience and, after making sure they're okay, says he's got some spare parts to fix the machine (or so he hopes). The viewers are then antagonized by obstacles such as Wayne's wife, Diane, fainting upon seeing the tiny people and Nick, Adam taking a picture of them with a blinding flash and picking up the theater to "show the little people to Mommy." The whole room is lifted right off its construction for a minute or two before Diane (who regained consciousness) and Channing persuade Adam to put the theater back where he found it. Then Nick's snake, Gigabyte, much larger than the miniature audience, nearly eats them (as he had not yet been fed that day). Quark, the Szalinski's dog, then chases him away with a few barks. Luckily, Wayne fixes the machine just in the nick of time and returns the audience and Nick back to normal size, but Quark is momentarily affected by the beam and then runs backstage out of sight.
Wayne accepts his award and begins his speech, but he is interrupted by Nick warning of a "big, humongous problem." The now giant Quark walks out onto the stage and the curtain closes while viewers hear the Imagination Institute's crew trying to stop him from crushing the place. He then finds his way through the curtain and sneezes on the audience for the finale. As they leave, the audience can hear the commotion from backstage continue.
The movie was presented in 3D by using polarized glasses and projectors.
The entire audience is on a platform that moves up to four inches high during the presentation to simulate the theater moving and the floor shaking (when Adam Szalinski picks it up).
The song "True Colors" is played as part of the pre-show film as an advertisement for Kodak. In Disneyland & EPCOT, the song is sung by two unknown artists. In the Disneyland Resort Paris version, it is sung by Cyndi Lauper.