To save her ill son, a field mouse must seek the aid of a colony of rats, with whom she has a deeper link than she ever suspected. Mrs. Brisby, a widowed mouse, lives in a cinder block with her children on the Fitzgibbon farm. She is preparing to move her family out of the field they live in as plowing time approaches, however her son Timothy has fallen ill, and moving him could prove fatal. Mrs. Brisby visits The Great Owl, a wise creature who advises her to visit a mysterious group of rats who live beneath a rose bush on the farm. Upon visiting the rats, Brisby meets Nicodemus, the wise and mystical leader of the rats, and Justin, a friendly rat who immediately becomes attached to Mrs. Brisby. While there, she learns that her late husband, Mr. Jonathon Brisby, along with the rats, was a part of a series of experiments at a place known only as N.I.M.H. (revealed earlier in the story as the National Institute of Mental Health). The experiments performed on the mice and rats there boosted their intelligence, allowing them to read without being taught and to understand things such as complex mechanics and ...
Timothy Brisby, now Timmy, leaves his family to train with the rats of NIMH in Thorn Valley. He meets Jenny, a mouse about the same age as he, who reveals her family are part of "The Lost Six" who did not escape NIMH. Timmy suspects his missing brother is also being held at NIMH and embarks on a rescue mission with Jenny while encountering old and new friends along the way.
