Siblings Margaret and Casey Brewer are playing Frisbee outside on a warm California winter day. Casey attempts to throw the Frisbee at their father. But he gruffly declines, because he has too much work to do in the basement. Casey and Margaret's father is a scientist. Ever since he got fired from PolyTech, their botanist father has been hanging around the basement, experimenting with plants. When Margaret tries to go down to the basement to see her father, he holds a bloody hand up to the light and utters, "Stay out of the Basement...". Casey and Margaret's mother, Mrs. Brewer has to leave for Tucson to visit her sick sister, and Mrs. Brewer reminds Casey, Margaret, and even Margaret's friend Diane to be nice to Dr. Brewer and make sure he eats meals.
Once Dr. Brewer emerges from the basement, his hand still bandaged, and takes Mrs. Brewer to the airport, Margaret gets a great idea: they should go inside the Basement and go investigate Dr. Brewer's secret experiments. Casey would rather watch the action movie that he rented. Eventually the three children make their way down into the basement. It is stacked with large tall plants of many variations, some bearing fruits, all very large for plants that supposedly had only been growing for a few weeks.
Casey strips down to his waist, feeling terribly hot, and leaves his shirt there. Casey notices a large glass contraption similar to a phone booth hooked up to a generator in the corner. He walks over to touch it and his bare body jolts with electric shocks. After admonishing him for his "hilarious" prank, by tickling his bare chest and stomach, the girls stop and listen to the plants, which sound like they are breathing. The tendrils of some of the plants begin to sway, as if beckoning the children towards the plants, and indeed some of the plants were heaving, as if in breath. The children wisely decide to stay out of the basement after all, and scatter out just as Dr. Brewer pulls up in the driveway.
Suddenly Casey, looking down at his bare chest, remembers that he left his shirt down in the basement! He quickly runs down to retrieve it, while Dr. Brewer is stopped by their neighbor in the driveway. Casey spots his sweater next to one of the tendril plants. When he goes to retrieve it, the plant's arms grab him and hold him tight. Margaret comes down to rescue Casey and she manages to free him. As they make their way up the stairs, they run into Dr. Brewer. Dr. Brewer calmly sits them down at the kitchen table and tells them that one day he will explain everything in the basement and they will all go down together, but until that day, they are not allowed in the basement.
Even by that time, Casey still had not put his shirt on and was still bare-chested. The next morning, Dr. Brewer has installed a lock on the door. That afternoon, Mrs. Brewer calls Margaret to tell her that her sister's surgery did not go as planned and she will be staying in Tucson a few more days. Margaret tells her mother about the basement and how Dr. Brewer has started wearing a Dodgers cap at all times.
Mrs. Brewer tells her daughter that her father probably feels like he has something to prove to Mr. Martinez, his old boss who fired him. After getting off the telephone with her mother, Margaret heads downstairs and spies her father in the kitchen, eating something from a plastic bag.
She stays hidden until he leaves, and when she retrieves the bag, she discovers it is plant food! She tells Casey about this as she makes him a peanut butter and jelly sandwich, but he does not seem to think it is all that weird that their father would be eating fertilizer. He then mocks her by pretending to be the Incredible Plant Man and she is Weed Woman. A few days later, the two siblings and Diane are playing Frisbee, again.
Casey tosses a Frisbee at their father, who has emerged briefly into the sunlight, but it hits him in the head, knocking his Dodgers cap off and revealing green leaves growing on his scalp! Dr. Brewer finally sits down with his children and explains that the leaves are just a side effect-- a side effect to what, he will not say, but he does explain his experiments. He asks if the children are familiar with DNA.
He is trying to take animal cells and put them into plant cells to create hybrid plants that have never existed. The glass booths in the basement are his transports, and though he is real close to succeeding, he has not quite made it work yet. He then brushes off all the moral and ethical concerns of his children as he heads back to the basement. That night, Margaret again spies on her father in the bathroom. She watches him take off his bandage and the blood from his wound is bright green! She also takes a peek in his bedroom and notices that his bed is filled with moist dirt and crawling with worms.
The next afternoon, Margaret tells Casey all about her spying discoveries from the night before. Suddenly, Dr. Brewer appears and tells his children that he has made them lunch. The two are served what appear to be green mashed potatoes, and their father yells at them to eat it. Luckily for the children, the doorbell rings and Dr. Brewer leaves to talk to Mr. Martinez, who has stopped by to check on Dr. Brewer's progress.
The two children scoop their green food into the trash and tell their father that they ate it. The next day, Dr. Brewer tells his children he will be out for a few hours to help their neighbor install a sink. The children see this as their chance to once again not to Stay Out of the Basement. As soon as he leaves, Casey picks the lock and the two venture downstairs. They come across Mr. Martinez's suit, neatly folded and hidden near a table. Then they realize that neither saw Mr. Martinez leave the house after visiting yesterday.
The two hear footsteps above and realize their father has come back. The two emerge from the basement just in time to be caught by Dr. Brewer. He explains that Mr. Martinez simply got hot in the tropical climate of the basement and took off his suit and left without it. Dr. Brewer heads out to continue work on the sink. Before he goes, he threatens the children to "Stay Out of the Basement".
Later that day, the children hear sounds from the basement. When they arrive in the basement, they find something shocking: 2 of their fathers! One of them is a clone, caused by Dr. Brewer's experiments. Not sure which one is their real father, Margaret picks up a hatchet and cuts one of the fathers with a kitchen knife. Red blood gushes from his hand. Therefore, Margaret turns on the clone and attacks and kills it with the hatchet.
One week later, Dr. Brewer is burning all of his plant's plants in his yard. He tells his children that he wants to discontinue his experiments permanently. Meanwhile, one of the smaller plants begins to prod Margaret with its leaves while whispering "Margaret, help me...I am your real father!"
The television adaptation of Stay Out of the Basement has several notable differences from the book. These include:
- Margaret knows who her real father is, when he calls her "Princess", her old nickname.
- They kill the plant clone with a can of weed killer, instead of a hatchet.
- At the end, Margaret overhears many plants whispering, claiming to be her father, instead of just one.
- Margaret's friend Diane was never mentioned.
- The original cover illustration featured a green plant monster hand opening a door, while a revised cover illustration featured a clothed plant monster in full view using chemistry equipment.
- The cover for the Classic Goosebumps reprint is an homage to the original cover.
- The title is an allusion to the 1973 film The Forgotten, which was also released under the title Don't Look in the Basement.
- Margaret and Casey's father was mentioned by his first name in the book: Michael Brewer.
- This is the first Goosebumps book to have the third narration.
- Rebecca Henderson, who played Margaret Brewer in the television episode, also played Kareen Hawling in Season 4's How I Got My Shrunken Head.
- This television episode and its continuation have been released on VHS. Both parts were also released on DVD, along with A Night in Terror Tower.
- R. L. Stine selected Stay Out of the Basement to be one of the first Goosebumps television episodes, as he wanted to ensure that his favorites were made into television episodes.