Viewers entered the Imagination Institute's theater for the Inventor of the Year Award Ceremony, in which professor Wayne Szalinski was receiving the award. Attendees were asked to don their "safety goggles" in preparation for the scientific demonstrations. The show opened with the crew of the show searching for Wayne, when he suddenly flew on stage miniaturized and in a transportation device called a Hoverpod.
He accidentally dropped the control box and sent the machine flying off behind the stage out of control. The Hoverpod came back and shorted 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 demonstrated some of his father's other inventions to kill time while the crew searched for him. Wayne's youngest son, Adam, put a mouse in his father's copy machine and they quickly multiplied (in an animation designed by Curious Pictures). This did not go smoothly, and the audience ended 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 went awry, Wayne managed to use his shrinking machine to return himself back to normal size. He brought out the machine to demonstrate its uses by shrinking a family's luggage, saving space and money when traveling.
Unfortunately, the machine went out of control and shrunk the audience (plus Nick, who pushes Dr. Channing out of the way of the machine's electrobeam). Wayne inspected 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 were 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 was 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 ate them (as he had not yet been fed that day). Quark, the Szalinski's dog, then chased him away with a few barks. Luckily, Wayne fixed the machine just in the nick of time and returned the audience and Nick back to normal size, but Quark was momentarily affected by the beam and then ran backstage out of sight.
Wayne accepted his award and began his speech, but he was interrupted by Nick warning of a "big, humongous problem." The now giant Quark walked out onto the stage and the curtain closed while viewers heard the Imagination Institute's crew trying to stop him from crushing the place. He then found his way through the curtain and sneezed on the audience for the finale. As they left, the audience could hear the commotion from backstage continue.
The movie was presented in 3D by using polarized glasses and projectors.
The entire audience was on a platform that moved up to four inches high during the presentation to simulate the theater moving and the floor shaking (when Adam Szalinski picked it up).
The song "True Colors" was played as part of the pre-show film as an advertisement for Kodak. In Disneyland & EPCOT, the song was sung by two unknown artists. In the Disneyland Resort Paris version, it was sung by Cyndi Lauper.