The film begins with Chip (Jay Underwood), the android, installing specially-ordered software designed to enhance his facial expressions; it is later discovered that he also inadvertently intakes a computer virus that causes him to malfunction very gradually, diminishing control over his own system's functions. Initially, the virus simply causes Chip to have momentary memory lapses resulting in poor judgment, but within three days it will completely destroy his internal systems, wiping his memory. That same day, Dr. Jonas Carson (Alan Thicke) and his daughter, Becky (Robyn Lively), attend Chip's high school graduation. Chip mentions that he wants to attend college and has already signed up for the summer session; however, his father does not feel Chip is ready to be on his own. Later, Dr. Carson finds Chip standing motionless in his room with a note attached to his shirt that says he has turned himself off and does not want to be turned back on until his dad agrees to let him attend college. Becky enters the room and manages to persuade her dad to grant Chip's request, and Chip suddenly turns to them and says "Thanks, Dad", revealing that he had merely been acting like he had turned himself off.
Since Dr. Carson only reluctantly agreed to allow Chip to attend college, he and Becky secretly follow him to the school in a vehicle that is set up as a monitoring station in order to watch from a distance. At the school, Chip sees a girl in a lab coat passing through the hall and becomes infatuated with her. The next day, he follows Roberta (Katie Barberi) into the robotics lab and asks her out on date, where she informs Chip that she is an android. Excited by this revelation, Chip tells her that he is also an android. Chip soon learns that Roberta is not able to decide anything for herself, so he introduces her to the concept of free will by reprogramming her. When Roberta chooses to go with Chip instead of returning to Dr. Phil Masters (Greg Mullavy) and the other scientists who developed her, the two of them are forced to flee. Prof. Victoria Gray (Dey Young) discovers that her fellow scientists are responsible for distributing a virus designed to disable competitors' androids, so she joins Dr. Carson in trying to catch up with Chip to provide the antidote.
After being relentlessly pursued a great distance, Chip and Roberta finally manage to escape the scientists, and they are surrounded by desert when Roberta explains that running has used up almost all of her power. With the virus's effects growing more pronounced, Chip is unable to control his body very effectively as he carries Roberta and desperately searches for a power outlet to recharge her. Not finding an adequate power source, Chip slumps to the ground as the virus overtakes him, saying haltingly to Roberta, "I... love... you." Dr. Carson and Becky arrive just a moment later with Prof. Gray, and they manage to successfully administer the antidote just before Chip's systems fail completely. Once he is fully revived, Chip reveals that he had utilized his magnetic finger to write all of Roberta's programming and memories to a diskette before she lost all power, preserving the character and personality of the girl that he had fought to protect. A photograph at the end shows the Carsons together with Roberta and Prof. Gray.
In each of the three Not Quite Human films, Chip is at a distinct level of development in his social awareness. While Chip had difficulty carrying on a sensible conversation in the first film and didn't notice how people perceived him, in Not Quite Human II he communicates fairly well but just takes some statements too literally. For instance, when a restaurant waiter asks if the group enjoyed their leek soup, Chip scans the floor and asks "Did I leak soup?" He also sometimes comes close to inadvertently revealing that he is an android, such as when he successfully chases his bus going at full speed down the road. It is this naivety and peculiarity that hinder Chip's efforts to form friendships. Chip's roommate, Brandon Wilson (Scott Nell), does his best to engage Chip in the social scene, but Chip still feels like an outsider. This is why Chip is so glad to encounter Roberta, another android who is also not very developed socially.
- Jay Underwood - Chip Carson
- Alan Thicke - Dr. Jonas Carson
- Robyn Lively - Becky Carson
- Greg Mullavy - Dr. Phil Masters
- Katie Barberi - Roberta
- Dey Young - Prof. Victoria Gray
- Scott Nell - Brandon Wilson, Chip's Room-Mate
- Mark Arnott - Moore, Dr. Masters' Assistant
- Mike Russell - Miller, Dr. Masters' Assistant
- Ty Miller - Austin, Bus Punk
- Eric Bruskotter - Rick, Bus Punk