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Nostalgia Critic tackles the themes of the Secret of NIMH: http://thatguywiththeglasses.com/videolinks/thatguywiththeglasses/nostalgia-critic/39603-nostalgia-critic-what-does-the-secret-of-nimh-mean
I like a lot of the points he raises, but I kinda view his stance on the Stone as a cop-out. The way I see it, yes, it can represent "the unknown", and it's interesting to think about it that way, but the Stone isn't necessary to evoke the unknown. There are already plenty of mysteries in NIMH, and they are generally mysteries that I find more interesting (like how do the Rats make their way in the world from here, what sort of lasting consequences are there for them, etc.). There is already a sense that the Rats must confront unknowns all the time due to their very nature.
I would have less of an issue with the Stone if some of these mysteries surrounding it were even acknowledged, but aside from Nicodemus's brief explanation of the source of it's power ("courage of the heart"), absolutely none of them are addressed in even a perfunctory way. We're just supposed to assume that of course the Rats have magical abilities. Why wouldn't they? It's weak storytelling for the sake of visual interest.