Mrs. Brisby, a widowed mouse, must find a way to move her family out of harm's way as plowing season approaches. Her son Timothy's illness makes this task even more perilous. Seeking advice, she visits the Great Owl and is directed to a group of rats living beneath a rose bush. There, she meets Nicodemus, a wise leader, and Justin, a friendly rat who befriends her. Mrs. Brisby learns about her husband's involvement in experiments at N.I.M.H., which boosted the intelligence of the mice and rats. The rats, including her husband, escaped and settled on the farm, creating an elaborate underground home. However, they're unhappy about their dependence on humans and plan to leave. They agree to help Mrs. Brisby, but a rival rat, Jenner, plots to kill Nicodemus during the move.

The Secret of NIMH
A mother mouse forms an unexpected alliance with a group of rats to rescue her ailing child, as they work together to uncover a cure.