Barney Snow (Elijah Wood) is an amnesia victim who resides at a Massachusetts advanced care facility for terminally ill youth. The only thing he remembers about the past is driving a red convertible and not being in control of the vehicle. Dr. Marie Harriman (Janeane Garofalo), a psychiatrist, tries to assure him that the experiments she and another doctor (Roger Rees) are conducting upon him will make him better.

Meanwhile, Barney manages to befriend Billy (George Gore III), who is afflicted with a genetic disease that will eventually shut down his kidneys, and Mazzo (Joseph Perrino), a young man with bone cancer. Since he can't live in the past, Barney can be really present to his new friends who all live in isolation. He finds himself attracted to Cassie (Rachel Leigh Cook), Mazzo's twin sister who feels cut off from her dying brother.

Martin Duffy directs this thematically rich drama written by Jennifer Sarja based on a novel by Robert Cormier. When Barney finds out the true nature of his predicament and the treatments he is receiving, he must make some important choices about the quality of his life. In The Bumblebee Flies Anyway, the parameters of health and healing are expanded to include memory, friendship, a finely finished death, and love.