The Lee of The Stone is a location in the Secret of NIMH and, more importantly, the final location of Mrs. Brisby's home.
The Lee of The Stone is a large stone protruding from the ground and arching over the cinder block in which the Brisby family resides. Because of it's unusual positioning, it more than likely proved to be an obstacle when moving the Brisby home. Actually, the placement of the home on the lee of the stone protected their home when the farmer plowed the field and drove other animals out of their homes or even killed them. By following the advice to move her home to the lee of the stone, Mrs. Brisby saved her children.
The name "Lee", in this context, is an old word for shelter or protect. So, the name is referring to the fact that the stone protects the Brisby home from the farmers plow when harvest season comes. The Lee side is also the side of a ship that faces down wind