Phoebe is a young girl, roughly twelve years old, who becomes the host for the miniature medical adventure at the center of the story. She is a friend of Geo, a boy about her own age who is clearly fond of her, and she also knows Kay, a medical student. She arrives in town to visit Kay rather than Geo, having slept through her in-flight meal and gone without food. After fainting in the research building lobby, she later wanders into the lab and, while hungry, eats cookies that contain a tiny ship with Geo and Dr. Brain aboard, accidentally swallowing them into her body.

In personality, Phoebe is energetic, rambunctious, and fun-loving. She is playful and easily bored, preferring to go off and do her own exploring instead of staying quietly in the lab, and she often treats her own body as a source of amusement rather than a subject of serious study. She is the most childish and least medically curious of the main characters, frequently disbelieving Kay when he explains facts about her health or reacting with disgust to what he tells her. Her obliviousness is a defining trait: she never realizes that Geo and Dr. Brain are trapped inside her, so she goes about her ordinary activities while they struggle to survive within her.

Her main motivation is simply to enjoy herself, satisfy her hunger, and follow her own curiosity in the wider world. She has no special powers or scientific expertise; her importance to the story comes from being the person whose body the travelers must navigate. Her everyday actions, such as eating, sleeping, and moving around, create the changing conditions and dangers that Geo and Dr. Brain must cope with, and Kay watches over her from outside as he works to rescue them.

In her relationships, Phoebe is the object of Geo's quiet affection, though she seems more interested in Kay, whom she came to visit. Kay cares for her wellbeing and checks on her condition, while Dr. Brain, the eccentric inventor trapped inside her, frequently analyzes her body's workings from within. Over the course of the story she shows some growth: although she begins as the least inquisitive character, by the time the journey reaches her nervous system she becomes more engaged as new connections form in her brain. Overall, she is a lively, spirited girl whose carefree nature serves as both a source of humor and a driving force for the adventure that unfolds inside her.