Mrs. Frisby became a widow last summer, but through a combination of "luck and hard work," she has managed to keep her family "happy and well fed." While three of her children remain healthy and content, the story unfolds with her son Timothy falling ill with pneumonia. The annual Moving Day is fast approaching, a time when all the animals must vacate the field before the plowing starts. If Timothy is taken to the woods with them, he risks succumbing to the cold. Determined to ensure Timothy's safety and warmth until he recovers, Mrs. Frisby embarks on a series of adventures. Although she longs for her late husband's help in resolving their challenges, she understands that the responsibility for her family's well-being falls on her shoulders.

Mrs. Frisby is a sensible and insightful character who focuses on resolving her issues rather than worrying about them. Despite her fears, she courageously ventures through cat territory, rides on the back of the bird Jeremy to visit the Owl, and seeks assistance from the rats' community. When captured by Billy Fitzgibbon, she realizes she must escape, not only for her own sake but also to protect her children and the rats. Her courage astonishes others, and the crucial information she provides to the rats ultimately saves their lives. Illustration by Zena Bernstein for "Mrs. Frisby and the Rats of NIMH" by Robert C. O'Brien. Atheneum: New York (1972). Although other characters, like Jeremy and the Owl, support Mrs. Frisby, it is the rats who ultimately rescue her home. Over a hundred rats reside in the community beneath the rosebush, but we become acquainted with just a few, notably the leader Nicodemus and the charming Justin.

Nicodemus shares with Mrs. Frisby the story of NIMH, where he and others were subjected to injections as part of a laboratory experiment. He explains that the scientists at NIMH were not deliberately cruel, but the mere fact of being caged made it unbearable, despite the cages being "not uncomfortable." After escaping NIMH, the rats use their newfound abilities to construct a technologically advanced society. However, they fear losing their freedom and plan to establish a civilization by farming and creating a self-sufficient community, rather than by stealing electricity or food. This plan faces resistance, as some rats are reluctant to give up their current comforts for the challenges of farming. Nonetheless, Nicodemus and most of the rats emphasize the value of freedom and self-reliance over mere comfort. This theme of freedom versus "captive" comfort is a recurring motif throughout the novel.

The characters in the story exhibit a blend of personal bravery and teamwork. Courage inspires action, and each character who assists another ultimately receives help in return. For instance, if Mrs. Frisby hadn't aided Jeremy, she wouldn't have encountered Owl or discovered how to save Timothy. Similarly, if the rats hadn't liberated Jonathan and Mr. Ages, they wouldn't have escaped NIMH. Later, by helping Mrs. Frisby, they managed to leave the rosebush just in time to save themselves. The narrative highlights the mutual reliance of the creatures. Additionally, it emphasizes life's unpredictability. From the outset, when Mrs. Frisby discovers the food of an animal that may have perished, to the conclusion, where two rats sacrifice themselves to save others, the fate of some animals remains unknown. Yet, despite this unpredictability, the world depicted is not unfair. The bravery of Jonathan, Mrs. Frisby, and the rats who stay behind underscores the importance of loyalty, friendship, and love.