Clearly, Shawn McDaniel is the protagonist of Stuck in Neutral, and through him the reader sees the other characters and the action of the story as it develops. Shawn is a rounded, fairly believable fourteen-year-old, given the premise that his physical problems leave him unable to communicate who he is and what he thinks. Shawn is a full human being, which is, of course, the point of the story. The portrayal of Shawn avoids mere sentimentalism. Shawn is no saint, wise beyond his years and purely good. He has likes and dislikes, a sarcastic sense of humor, crushes on girls, and he gets frustrated and angry. Mostly, Shawn is an adolescent wondering about his life.

Shawn has adjusted to what may seem impossible conditions in his life. In addition to the fact that he has absolutely no control over his body, he also experiences seizures. These seizures he describes as out-of-body experiences; they are actually positive because he loves the "feeling of escaping my screwed-up, worthless body." Shawn adds, "I love my seizures because they give me the kind of life I imagine normal people enjoy, and then some. They give me freedom." Shawn is actually very sensitive to what life has to offer. He enjoys warm, sunny days as well as rain. He can call up his own reactions to all the music he has ever heard. He learns much from TV, fantasizes about his sister's friend, Ally, and cherishes the memory of his father taking him on a virtual reality ride at the Pacific Science Center. He likes potato chips. He admires his brother, Paul, who protects him. Shawn also loves his mother, Lindy, who patiently cares for him, and his sister, Cindy. On the negative side, Shawn is aware of the pain his condition has caused his whole family. His father left because he could not handle Shawn's situation. However, Shawn clings tenaciously to life.

Shawn's father has written a Pulitzer winning poem about Shawn, and he suffers greatly over his son. Through the story, by listening to his father's comments, especially on a TV show about another man in the area who killed his disabled son, Shawn begins to suspect that his father is planning to kill him. Shawn seems to be sympathetic to his father and his motives, but he would choose life for himself. Shawn's love of life is central to the theme of the story. People cannot judge clearly whether others would want to die or not. Shawn thinks, "Memory is all we have, for ourselves and for the people we love. . . . Will anyone ever know that my life, once lived and over with, was one of perfect remembering? . . . I'm just not ready to give up the hope that someday I might be known. I'm not ready."

Shawn's father is the other main character in the story, a driven, assertive man who is angry about his son's condition. Shawn's dad, Syd, is very intelligent and compassionate. However, he can also be seen as "weak and cowardly," which is how Shawn's mother describes him. He could not bear living with Shawn so he left his family. Syd cannot stand the idea that Shawn is suffering inside himself. Juxtaposed against Syd's dark and confused suffering, however, is Shawn's intense internal life and his trust in his father. The end of the novel offers no simple answers, just the question: would it be right to end Shawn's life?