NIMH

NIMH (National Institute of Mental Health) were the central antagonists of the entire Secret of NIMH series and were based very loosely on a real-world organization of the same name, however the name is where the similarities end and the fictional NIMH is considered (at least by animals) as one of the most evil places in the world.

NIMH was responsible for the creation of the hyper-intelligent rats that would eventually become known as the "Rats of NIMH" and it was these rats that orchestrated a daring escape with the aid of several mice - having had enough of the continued abuse NIMH regularly put them through as part of medical experiments that were clearly not monitored correctly (for example they actively captured wild rodents for experimentation, a practice that is no longer widely practiced due to animal welfare (as well as the fact most reputable labs breed their own mice / rats).

NIMH is a faceless evil and is often mentioned rather than actually faced, though in the sequel NIMH would play a bigger role and arguably become the main antagonists of the film - in fact if one were to be picky one could argue NIMH was also the main antagonist of the original film as they had created Jenner (though, somewhat ironically, they also created Nicodemus and other "good" rats - who aided Mrs. Brisby in her quest).

It is unknown what became of NIMH after the series ended but it is presumably still active, whether or not it has improved its (to be frank) horrific treatment of animals is also left unknown.

Years later, Timmy comes across a female field mouse named Jenny McBride, whose parents were two of the lost nine mice who tried to escape NIMH but were thought to have died. The Thorn Valley council decides it would be too dangerous to save the nine mice, so Jenny and Timmy go alone. They take a hot air balloon, but it is attacked by a hawk and crashes in the forest.

Seeking help, they visit the Great Owl. They there learn that a caterpillar named Cecil has teamed up with Jeremy, the crow from the first film, to trick the forest animals into paying them money. Jeremy and Cecil take the two mice to NIMH where they find two of the rats from Thorn Valley, Justin and Brutus. They also learn that Dr. Valentine, the head scientist, has made Martin insane. After being made insane, Martin took over the lab and brainwashed Dr. Valentine with a device similar to the one Valentine used on him and made him think he was a dog. Martin plans to use an army of lab rats riding a flock of ravens to take over Thorn Valley.

He asks Timmy to join him, but he refuses and is locked in a cage as Martin drags Jenny away to make her his queen. Timmy escapes with the help of Cecil and they go to free Jenny. Together, they knock out Martin and Timmy tricks Martin's army of ravens and rats to fly in the wrong direction. Timmy and Jenny then leave to find the others, only to find once everyone is free that NIMH is on fire. The survivors (Timmy, Jenny, and her parents) flee. Timmy goes back to save Martin. Before he leaves, Jenny tells him she loves him and he tells her the same. After being attacked by the crazy cats once again, Timmy sends them down an elevator shaft and finally finds Martin.

Timmy and Martin are able to escape through the lab's skylight, with some help from Jeremy. Jeremy takes the survivors to safety while Dr. Valentine and the human employees of NIMH flee their headquarters and never returned.

Goals
To continue experiment on rats, mice, and other animals. To recover the rats and mice that escape from NIMH so they can learn from them. (Maybe to cover up their losses and if anyone find out about it, it will be trouble for NIMH) NIMH believes that their experiments have work on the rats and mice. The rats and mice, maybe, became more intelligent than men and they have science and possibly magic.

Trivia

 * NIMH is based on the real-life health institute.