The rats' effort to move the Brisby cinder-block home out of the path of the plow (by way of a rope/pulley system) is sabotaged by Jenner, who wanted to seize power from Nicodemus and convince the others not to leave the farm. Nicodemus is crushed by the collapsed machine. Jenner's plot is undone when Mrs. Brisby, who had been temporarily trapped in the farmer's house when she drugged the cat Dragon, arrives to tell the rats that exterminators from NIMH are coming in the morning to kill them. Realizing that she has also been bequeathed Nicodemus' mysterious stone, Jenner tries to kill her; Justin (Nicodemus' right hand rat) fights him off and declares that they will leave as soon as Mrs. Brisby's house is moved. Jenner is killed by his own reluctant henchman.
A greater danger now arises - the house begins sinking into the mud with Mrs. Brisby's children trapped inside. She and the rats are helpless to save it from total submersion despite their best efforts, and she almost drowns, losing the stone in the process...
...but only for a moment. Her heart's courage has already unleashed the stone's hidden power, and it flies out of the mire and back to her. Its supernatural energy flows into her as she takes it in hand, and from there she sends it into the ropes still tied around the house. This pulls it up and out, and finally moves it out of harm's way altogether, saving her family.
Come morning, the rats have left the farm for Thorn Valley (it's explained that Justin was given the stone, as Mrs. Brisby no longer needs it), where they will further develop their society without having to steal from humans.