The Secret of NIMH/WMG

Whatever NIMH injected into the rats and mice was contagious.
The animals in Fitzgibbon's field seem rather intelligent. Sure, it could just be typical cartoonish anthropomorphism, but perhaps the injection given to the rats and mice of NIMH was contagious somehow. The rats and mice got the concentrated dose, so they're far more intelligent, but Mrs. Brisby (whose mate was a NIMH escapee) and her family seem quite smart, even compared to their 'neighbors'. They have a fully furnished home and wear clothes (The Shrew picked up the habit, or perhaps caught the 'bug' from Mrs. Brisby). The Great Owl is so smart because he ate one of the rats of NIMH, thereby getting the 'full' dose (Hell, he even LOOKS a bit like Nicodemus).
 * Perhaps the intelligence is spread psychically. Nicodemus demonstrates telekinetic powers throughout the film; by extension, the enhanced rats and mice likely possess latent psychic talents that allow their exceptional intelligence to spread to those around them. It may be restricted to rodents and birds, since Dragon didn't show phenomenal intelligence even after eating Jonathan Brisby.
 * That would suggest Theory of Primary Perception in animal form, AKA everything is linked by psychic, unconscious bonds; and by extension Collective Unconscious. But something that can bring out latent psychic powers in ANIMALS would have humans swarming all over NIMH, and NIMH itself would quadruple its efforts to capture the Rats. Besides, it still doesn't sound entirely correct for mutations to occur by something simply being there and unconsciously making them happen.
 * The psychic powers are Canon. We see them. And that variety of mutation happens in cartoons quite often...
 * But psychic powers don't cause mutations themselves. Besides, wouldn't it be ridiculously painful for Mrs. Brisby to suffer the same kind of alterations the Rats did? Even through alternate means? Back to the Mantra.
 * It was ridiculously painful. Her hands were in bandages for quite some time after she used that locket.
 * True, but that was because she was holding sternly on to the locket even as he burned into her skin, right?
 * These mutations would have occurred around the time that the Rats of NIMH first arrived in the field. The delivery system is based on a passive psychic field; it would most likely be a gradual process rather than the rapid and painful mutation that the Rats experienced. Do you think this sounds bizarre enough?
 * Passive psychic mutations? Wouldn't ole' Nicodemus know about that?
 * Who knows? Maybe he did, and never got the chance to tell anyone before Jenner flattened him.
 * He decided to be sadistic and tell Brisby, "Your probably just like us now, but I'm going to tell you you'd have died first, and then told you the truth once we moved your house. Oops, I'm dead! Sorry 'bout that." Nicodemus must have had a layer of humor under all that mystery.
 * Covers both the "Why Mrs. Frisby/Brisby Had A Shorter Lifespan" and "Why No Extreme Pain Was Experienced": The pain was physically real, not a result of the neural network rewrite, and a result of the cells changing due to something in the injections that was not contagious, but would allow for inheritable increased lifespan and physical abilities. The intelligence side effect was something else in the cocktail of drugs and viruses. If it was contagious, it would only have mild flu-like or cold symptoms if anything (if thanks to the telepathy, it could have no symptoms, and Nicodemus simply didn't know of the effects). If it was not, then it could be a result of the animals being affected by their interactions with Johnathan and Mr. Ages, and indirectly through Mrs. Frisby and the children.

The Shrew and Mr. Ages used to be friends/had some sort of past affiliation.
It is implied in the movie that the super-intelligent animals of NIMH are capable of educating and to a degree civilising common wild animals. The evidence for this is Mrs. Brisby who is the only "normal" animal on the farm who wears clothes, lives in a house and can read, all of which are traits belonging to the animals of NIMH and all of which (presumably) were taught to her by her husband.

The only other seemingly "normal" animal who wears clothes is the Shrew. Whilst the movie never hints at how academically proficient she is, she still seems to have intelligence on par with Mrs. Brisby. It is my theory that Mr. Ages had done to her what Jonathan Brisby did to his wife and then fell out with her, as the Shrew seems to hold nothing but contempt for the rats and Mr. Ages.

Nicodemus isn't psychic, or even a wizard; he's one of the Inspired.
The NIMH experiments were an Inspired experiment to uplift mice, and the results were just a little too good; the rats (and two mice) got away. But not only were they granted intelligence, one of the rats achieved a full-blown Catalyst and became a Genius. Only a few dots in Apokalypsi (for the memory imager) and Epikrato (for the telekinetic amulet) are necessary to explain all the supernatural elements of the film. The rats aren't moving to Thorn Valley just to become self-sufficient, they need more room away from humans to really start creating Wonders without worrying about humans noticing.

In addition to Nicodemus' Inspiration, it's possible that Jonathan Frisby Catalyzed too; Nicodemus gives the amulet to Mrs. Frisby, telling her that Jonathan wanted her to have it.

The Great Owl is Mandos
Manw Ã« and the other Valar got pretty much insane, and somehow managing to return to the real world because of the Artifact of Doom Mrs Brisby/Frisby. The process in which the rats gain conscience in NIMH somehow mimiced the way the eÃ¤ were given to men and the old middle-earth races, and the Valar perceived that as going against Eru's will and possibly done by corrupted Ainur, so the help provided by the owl/Mandos was all part of a plan to eliminate all the rats, mice and other sentient creatures.

The Great Owl is Nicodemus
They look so darn similar, so TGO is a shape shifted Nicodemus. that's why he didn't eat Mrs. Brisby.
 * Creators did this for fun, to add more mystery than the poor movie could hold ZOMG sause

The story could be set in the world of Assassin's Creed
Obviously, I don't believe this is true, but it's possible.

Think about it; how would an injection suddenly give the rats the ability to read? NIMH could very well just be a wing of Abstergo doing animal research on implanting Genetic Memory; in this case, giving non-humans the ability to read by implanting them with human memories. The amulet could also be a portion of one of the Pieces of Eden (Probably a piece they salvaged from the one that was destroyed), which would explain its unusual powers. Abstergo had it at NIMH (Maybe to test its effects on the animals or something), the rats found it while they were escaping, and, figuring it was special somehow, brought it with them. Could overlap with the theory about the injection being contagious if a viral vector was used to implant the genetic memories.


 * As far as the rats having the ability to read, only Nicodemus demonstrated that ability- kind of justifiable considering he's psychic. But otherwise, it's a pretty good theory.

The scientists were trying to make an true intellagence boosting drug.

 * They always seemed a bit...dodgy, because generally lab rats are pet rats, not wild ones. So they must have not wanted any one knowing one knowing what they were doing. They were not trying to produce a memory or learning drug, but one which may harshly seperate humans with the drug to those without, like the normal rats from the NIMH rats.

The Secret of NIMH happens in the same world as the old Land of Giants TV Show.

 * I just can't get this idea out of my head. It explains why such small animals as mice and rats have human level intelligence -- they are human size, it's the world AROUND them that's oversized. And the treatments at NIMH? They gave the rats a mental boost, but not as much as you'd think. If humans from the "normal" world got there, they'd find themselves the same size as Mrs. Brisby and Justin and the rest... and probably chased by NIMH as well.
 * Wait...why would being human-size give the rats human intelligence levels?
 * that would give them just about human-sized brains as well.

The reason Martin gets over being turned insane in NIMH 2 is because the rats gave him a prefrontal lobotmy

 * Hence the bandage on his head.

The reason Mrs. Brisby isn't given a first name is because she had no name prior to meeting Jonathan.

 * Naming conventions are just something the rats of NIMH picked up from humans. Johnathan wanted his children to have names so that's why they have them.

At least one more mouse of NIMH survived and became one of Gadget Hackwrench's parents.

 * Think about it. The nine mice of NIMH that didn't make it through the air vents were officially pronounced dead because those who escaped to Fitzgibbons' farm didn't have the time to retrieve their corpses and confirm their deaths. At least one got away alive but unseen by the official group and had a family afterwards. This also explains Gadget's way-above-average IQ.
 * Its been suggested that her immediate father, Geegaw, was that mouse. He not only survived the air vent trip, but loved the experience and took up flying because of it.

This movie, An American Tail, The Land Before Time and All Dogs Go To Heaven take place in the same universe, and form a loose quadrilogy.

 * It is unclear when exactly the film takes place, but An American Tail takes place in 1885 and All Dogs Go To Heaven takes place in 1939. It is possible that the film takes place somewhere in between those two movies. Because the more intelligent cats were sent away in Tail it may explain why Dragon behaves so animalistically, and it will also explain why animal intelligence is so common in Dogs. At the very least, it is a nice thought.
 * However the sequels may also be taken into account, in which case this theory falls apart.
 * Would you really miss them if you were to follow this theory? Basically, it requires you to do that, and it is made easier by the fact that Don Bluth didn't make the sequels. So this theory may still work when taking that stand.

Nicodemus' "Prophecy" in the sequel actually applied to Martin, Not Timmy
So, "a son of Jonathan Brisby" will save the rats from the evil of NIMH, will he? Who was it, again, that managed to turn the tables on Valentine? That's right, Martin. Just because he turned temporarily evil doesn't mean his actions didn't benefit rodentkind as a whole. Jenny and Timmy get points for saving him, naturally, but Martin was the only genuine Chosen One.