Timothy Frisby, a field mouse, teams up with the adventurous young rat Racso as together they try to prevent the destruction of a secret community of rats that can read and write.

When two brothers steal a rabbit from a back yard in the rich part of town, the incident brings about their collision with other children from a background very different from their own.

Lost in the North Woods, Margaret and her shy, mute brother, RT, are saved and nurtured by the rats of NIMH, but a return to civilization could mean the end of the world of NIMH should the children divulge the secret of their rescue.