Timmy, son of the famous Jonathan Brisby who helped saved the rats from NIMH, has decided to leave his mother, brother and sisters on the farm and head to Thorn Valley where the Rats of NIMH have their new home. There he attempts to learn all he can to become a heroic mouse like his father. He also meets Jenny, a girl mouse who says her parents were among the mice at NIMH who had been presumed dead all this time. Now it's up to Timmy and the Rats to save the mice from NIMH or end up as lab subjects themselves...