There are two problems solved in Mrs. Frisby and the Rats of NIMH: Mrs. Frisby's and the rats'. The rats are able to get Mrs. Frisby out of her predicament by moving her cinder block house behind a stone so Mr. Fitzgibbon's plow will not pass over and destroy it. To make sure Dragon will not be a threat to her family during the night, Mrs. Frisby drugs the cat's dinner.

The solution to the rat's problem—whether or not they should leave the comfort of the rose bush and live independently in Thorn Valley—comes when Mrs. Frisby informs them that NIMH is coming after them (she overheard the Fitzgibbons discussing this when she was imprisoned in the house). The rats take out everything they need (food, tools, etc.), destroy any signs of their advanced civilization, and then fill the inside of the bush with trash to make it look like an ordinary rathole. To complete the illusion, ten rats, including Justin, stay behind to fool the scientists.