Dr. Brainard, a long-retired scientist, has just finished breakfast and the morning newspaper. He puts all of it in a special bin and we watch it move on a conveyer belt out of his house and into the backyard. Along its path, shrink rays miniaturize the objects and they continue down an even smaller conveyer belt into the Szalinski kitchen.

We discover the Szalinski home is actually a miniaturized structure in the greenhouse behind Dr. Brainard’s house. After the incident in Vegas, Wayne took his work from Sterling Labs and disappeared with his wife Diane and son Adam. They’ve spent years in seclusion, hiding themselves and Wayne’s inventions away from organizations who’d like to get their hands on his technology.

Adam, a 30-year-old-bachelor still living at home, is a promising scientist. Having earned online degrees in both mechanical engineering and computer engineering, Adam has built some marvelous machines, making his father proud, but he’s failed to venture out into the world on his own, which upsets Diane.

One morning, Dr. Brainard’s breakfast care package doesn’t show up, and Wayne can’t reach him on the radio. They decide to let Adam investigate. Adam reports that Dr. Brainard is missing and thinks he may have been kidnapped. Adam brings in the authorities, but when questions turn to who he is, Adam panics and flees the scene.

One of the police is Officer Terrence Whitaker, an older detective that specializes in runaways and victims of abusive homes. He senses that Adam, despite being a 30 year old man on the surface, has a childlike innocence and may need his help.

Alone and scared, Adam finds help from a woman who happened past him on the side of the road and offers him a ride. They check into a motel, where Samantha tells him she’s on the run as well, but from an abusive husband. Adam confides in her who he really is, the giant kid that stomped all over Vegas, and she asks if he can still grow in size (blatant sexual joke here, but Disneyfied for younger audiences.)

She says she’ll help him get home if he helps her hide, proposing that she could be shrunk and live in the greenhouse. Adam says that this would be perfect, as one of the reasons he never left home is because he didn’t want his parents to be alone with no neighbors or friends their size.

Meanwhile, mom and pop Szalinski are worried their son hasn’t returned or updated them on the situation. They can see people moving through Dr. Brainard’s house, some even investigating the green house. They hideaway, hoping the house will be mistaken as decoration, but one man isn’t fooled. Dr. Charles Hendrickson, Wayne’s old co-worker from Sterling Labs has never gotten over losing the size alteration technology, and suffering humiliation from Wayne Szalinksi, and after confirming his suspicions of Wayne’s location, he’s there to get revenge.

Wayne and Diane escape on a customized RC helicopter they stashed for just such a getaway. They are hunted down by drones controlled by Sterling security, crashing into a nearby park just as they spot Adam sneaking into the backyard. Adam sees Dr. Hendrickson taking off with their house and asks Samantha to follow him back to Hendrickson’s secret lab.

In the lab is Dr. Brainard, tied up and shocked to see the Szalinski home under Hendrickson’s arm. The mad scientist tells Brainard that if he can’t find Wayne, he’ll just take everything so that Wayne has to come to him. What he doesn’t know is that Wayne has spent the years perfecting his size alteration technology, which is of course now small enough to fit into a pocket, Wayne’s pocket.

Wayne and Diane enlarge themselves and head back home. They see they have no home to return to and police are still at Brainard’s, but luckily they find Samantha’s wallet in the grass, dropped when she and Adam were chasing after Dr. Hendrickson. Their only clue, but no means to find more information, they shrink themselves again and sneak Samantha’s ID in where the cops will find it. Once they do, they call in to get more details, and the Szalinskis overhear that Samantha is a known jewel thief and that her car was recently spotted in the old warehouse district.

Unbeknownst to the police, the Szalinskis hitch a ride to the area inside Officer Terrence Whitaker’s cruiser. When Officer Whitaker arrives to find Adam and Samantha sitting in her car, he goes to radio for backup only to see the car and passengers seemingly disappear. The Szalinskis know what has really happened, understanding that Adam must have taken a size alteration device along with him.

To Whitaker’s compounding shock, the Szalinski’s suddenly appear in his vehicle and they quickly explain to him who they are and what’s happening. He says he can’t go into the warehouse without a warrant, so the Szalinskis are on their own. They get out and shrink themselves to sneak into the warehouse.

Both sets of shrunken couples are inside Hendrickson’s lab. They don’t know that it was a trap, and Adam and Samantha are captured in a tiny box and Hendrickson sees the tiny device fall from Adam’s pocket. He is able to pick it up with tiny robotic implements and accidently sets it on himself, where he grows to incredible height. Seeing the threat the crazy scientist poses, Wayne enlarges himself to equal size and the men have an epic fight, crushing buildings Godzilla style.

Diane helps the others escape, Wayne defeats Hendrickson, and Samantha thanks the family. She confesses that she wanted to use the enlargement device to increase the size of her stolen jewels, but also says she stole them from her husband, not a store. It was the only thing she could grab of value to support herself when she left him.

Officer Whitaker believes her but says he can do little to help her. Adam, however, comes up with a plan. We cut to the future where Officer Whitaker is escorting a woman and her kids to a place outside of town. They enter a small shack where they are shrunk, revealing a tiny entrance that opens up on an expansive neighborhood contained within a greenhouse-like structure, each house containing a family now saved from their former lives of abuse. The Szalinskis greet the newcomers, Adam and Samantha delivering a basket of oversized fruit and a mini-bar bottle of champagne.