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, as he has too much work to do in the basement. Casey and Margaret's dad 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 the titular line, "Stay out of the Basement...". Casey and Margaret's mom, Mrs. Brewer has to leave for Tucson to visit her sick sister, and Mr. 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, Diane gets a great idea: they should go inside the Basement, and go investigate Dr. Brewer's secret experiments. Casey would rather watch his action movie that he rented. Eventually the three children make their way down into the basement, which 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 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 body jolts with electric shocks. After admonishing him for his "hilarious" prank, 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 afterall, and scatter out just as Dr. Brewer pulls up in the driveway.Suddenly Casey remembers that he left his sweater 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 tendriled plants, and 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'll explain everything in the basement and they'll all go down together, but until that day, they are not allowed in the basement. 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 didn't go as planned and she'll be staying in Tucson a few more days. Margaret tells her mom 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 phone 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's plant food! She tells Casey about this as she makes him a peanut butter and jelly sandwich, but he doesn't 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's 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 kids and explains that the leaves are just a side effect-- a side effect to what, he won't say, but he does explain his experiments. He asks if the kids are familiar with DNA. He's 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's real close to succeeding, he hasn't 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 peak 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's made them lunch. The two are served what appears to be green mashed potatoes, and their father yells at them to eat it. Luckily for the kids, 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 kids scoop their green food into the trash and tell their father that they ate it.The next day, Dr. Brewer tells his kids he'll be out for a few hours to help their neighbor install a sink. The kids see this as their chance to once again not Stay Out of the Basement and 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, and the two realize that neither saw Mr. Martinez leave the house after visiting yesterday. The two hear footsteps above and realize their dad's 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 with out it. Dr. Brewer heads out to continue work on the sink, but before he goes, he threatens the kids 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. 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 plants plants in his yard. He tells his children that he wants to discontinue his experiments permenantly. Meanwhile, one of the smaller plants begins to prod Margaret with its leaves while whispering "Margaret, help me...I am your real father!".