A widowed field mouse must move her family -- including an ailing son -- to escape a farmer's plow. Aided by a crow and a pack of superintelligent, escaped lab rats, the brave mother struggles to transplant her home to firmer ground.

The rats and mice, made intellectually superior in the original Secret of N.I.M.H., return to Thorn Valley to groom their destined leader - young Timmy Brisby.