A prophecy foretells that one of the children of Mrs. Brisby [Debi Mae West] and her late husband, Jonathan, will save Thorn Valley from NIMH. Brisby's youngest son, Timothy [Ralph Macchio], is chosen, but his older brother, Martin [Eric Idle], believes he should have been. Martin decides to prove his worth and heads off to seek his own adventure, testing the family’s fate from a distance. Timmy’s journey begins when Jeremy, the Brisby’s longtime acquaintance, [Dom DeLuise], carries Timmy by air to Thorn Valley, a place brimming with new faces and unfamiliar rules.
Upon arrival, Timmy is warmly received by Thorn Valley’s residents and quickly becomes a pupil under Justin [William H. Macy], the capable leader of the Rats of NIMH, and Mr. Ages [Arthur Malet], the wise elder who guides Timmy’s training. Through years of practice, Timmy learns to face challenges by adapting, improvising, and thinking on his feet. He dreams of becoming a hero on par with his father, yet his path is shaped by a stubborn streak that makes him reluctant to follow orders or slow down to consider the consequences.
A fragile alliance forms when Timmy meets Jenny McBride [Hynden Walch], a female mouse whose parents were among those who once tried to escape NIMH and were believed dead. Jenny reveals that her family survived, though they have been trapped since, and she warns that the institute has a secret plan unfolding on the next full moon. Despite Thorn Valley’s council warning that saving the trapped mice is too dangerous, Timmy’s resolve strengthens after learning that Martin has also been captured.
The rescue plan begins with a makeshift hot air balloon, and Timmy and Jenny set out on a bold mission. Their journey is interrupted when a hawk attacks, sending the pair crashing into the forest. There, they encounter Cecil [Meshach Taylor], a caterpillar with a knack for scheming who initially poses as a friend but proves to be a con artist. Cecil’s arrival marks a turning point, as he distracts their pursuers just long enough for Timmy and Jenny to regroup.
Seeking true aid, the duo seek out the Great Owl, only to discover that Jeremy has been masquerading as the legendary bird. Timmy and Jenny learn that Cecil has aligned with Jeremy to fleece forest animals out of their money, a deceit that is exposed after a tense confrontation. With the illusion shattered, the group presses on and makes their way toward NIMH, hoping to confront the institute’s troubling experiments firsthand.
Inside NIMH, they uncover a disturbing sight: experiments that have turned rats and other creatures into obedient minions, while the human scientists themselves drift toward a more animalistic nature. Timmy and Jenny reunite with Justin and the rats, who have come to aid in the effort. Timmy is assigned to guard duty, but he abandons his post in a bid to find Martin, and the group is promptly captured by a pair of mangy cats, Muriel [Andrea Martin] and Floyd [Harvey Korman].
The captives are brought to the head scientist, Doctor Joseph Valentine [Steve Mackall], only to confront a startling truth: Martin is the true mastermind behind the plot. Valentine has been using a brainwashing device to drive Martin’s cleverness, and in turn, Martin has managed to brainwash Valentine and the others. Martin plans to lead an army of lab rats riding a flock of pigeons to seize Thorn Valley, and he tries to recruit Timmy to his side. Timmy, true to his core, refuses and is kept detained as Jenny is dragged away to become Martin’s queen while the rats are imprisoned.
Hope surfaces when Cecil returns to the scene with a renewed resolve to help. Timmy escapes, sets a trap for Muriel and Floyd, and heads back to rescue Jenny while Cecil frees the captive rats. The rescue is hard-fought, but Timmy ultimately defeats Martin and misdirects his aerial army, sending the flocks off course.
As Timmy and Jenny press on, a fire threatens everyone, forcing a desperate flight from the collapsing facility. He returns to save Martin, a moment marked by a quiet confession of love between Timmy and Jenny. Muriel and Floyd renew their pursuit, but Timmy fends them off, pushing the threats into an elevator shaft to meet their end. With the lab’s skylight as a last exit, Timmy and Martin make their escape, aided by Jeremy who guides them to safety. They return to Thorn Valley, where Martin has begun to regain his sanity, and Timmy receives a hero’s welcome from the grateful valley. The prophecy is fulfilled as Thorn Valley celebrates Timmy’s resilience, his family’s relief, and the restored harmony of their world.
