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The Secret of NIMH
Mrs. Brisby, a widowed field mouse, lives in a cinder block with her children on a farm owned by the Fitzgibbons family. She intends to move her family out of the field as plowing time approaches, but her son Timothy has fallen ill, making it impossible for him to travel.
Brisby visits Mr. Ages, a friend of her late husband Jonathan, who diagnoses the illness as pneumonia, provides her with medicine, and warns that Timothy must stay inside for at least three weeks to recover. On her way home, Brisby befriends Jeremy, a clumsy but amiable crow, shortly before they narrowly escape the Fitzgibbons' cat, Dragon. The next morning, she discovers that the plowing has begun early. Although her neighbor, Auntie Shrew, helps disable the tractor used for the task, Brisby realizes she needs a better plan. Jeremy then takes her to meet the Great Owl, who at first rejects her, but upon learning she is Jonathan Brisby’s widow, tells her to visit a colony of rats living beneath a rose bush on the farm and seek out Nicodemus, their wise and mystical leader.
Brisby enters the rose bush and encounters an aggressive guard rat named Brutus, who chases her away. She is led back in by Ages and is amazed to see the rats' use of electricity and other technology. Brisby meets Justin, the friendly captain of the guard; Jenner, a ruthless and power-hungry member opposed to Nicodemus; and finally Nicodemus himself. From Nicodemus, she learns that many years ago the rats, along with her husband and Ages, were part of a series of experiments at the National Institute of Mental Health (NIMH for short). The experiments gave them human-like intelligence, enabling them to escape, as well as extending their lifespans. They are unable to live as typical rats would, however, and need human technology to survive, which they can get only by stealing, placing them at great risk of discovery. To avoid being at the mercy of humankind again, the rats have collectively decided to leave the farm and live independently in an area they refer to as Thorn Valley. Nicodemus then gives Brisby a magical amulet that will activate when the wearer is courageous. Meanwhile, Jenner, who wishes for the rats to remain in the rose bush, plots to eliminate Nicodemus.
Out of respect for Jonathan, the rats agree to help her move her home. First, they need to drug Dragon so it can be done without interference. Only Brisby can do this, as the rats cannot fit through the hole leading into the house; Jonathan was killed by Dragon in a previous attempt, while Ages broke his leg in another. That night, she puts the drug into Dragon's dish, but the Fitzgibbons' son catches her. While trapped in a birdcage, she overhears a telephone conversation between the Fitzgibbonses' patriarch and the staff of NIMH and learns that the institute intends to exterminate the rats in the morning. Brisby then escapes from the cage and runs off to warn them.
As a thunderstorm approaches, the rats begin moving the Brisby home, with the children and Auntie Shrew inside, using a rope and pulley system. Jenner sabotages the assembly, causing it to fall apart and crush Nicodemus to death. Brisby soon arrives to warn the rats about NIMH's arrival, but Jenner attacks her and attempts to steal the amulet as his reluctant accomplice, Sullivan, alerts Justin, who comes to Brisby's aid. Jenner mortally wounds Sullivan and engages Justin in a sword fight, but is killed by a knife in the back from the dying Sullivan.
The Brisby home begins to sink into the muddy ground and Brisby and the rats are unable to raise it. All appears lost until Brisby's will to save her family suddenly gives power to the amulet, which she uses to lift the house and move it to safety. The next day, the rats, with Justin as their new leader, have departed for Thorn Valley as Timothy begins to recover, while Jeremy meets and falls in love with an equally clumsy female crow.