Mrs. Brisby, a timid field mouse and widowed mother, faces a dire predicament as her young son Timothy falls gravely ill just before the annual plowing of the fields. To save him, she must move her family to a safer location, but her journey is fraught with danger. Seeking help, she visits the Great Owl, who advises her to seek out the mysterious rats of NIMH. These highly intelligent rats, led by the wise Nicodemus, live beneath a rose bush on the farm and have a secret connection to her late husband Jonathan.

Mrs. Brisby discovers that the rats of NIMH, once captive in a laboratory, have developed extraordinary abilities and a sophisticated society. Nicodemus explains their shared history and offers both assistance and a magical amulet to protect her. As the plot thickens, Mrs. Brisby must navigate a series of challenges, including betrayal within the rat community and external threats, to ensure her family's safety. Her courage and resourcefulness are tested as she discovers the depth of her own strength and the true legacy of her husband.