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I've done my silly quota for the month, now time to actually try and spark up something.
This is a 'what if' question, so it's not like it's supposed to be a 'real' interpretation or anything. It's just for fun.
What if after Mrs. Brisby gets the medicine from Ages and delivers it to Timothy, she dreams the rest of the movie and the ending is her waking up.
Think about it for a minute. The book makes this possibility a bit more plausible than the film, but the film does have hints that it's a dream.
She faints after using the stone. Now she claims to have given the stone to Justin afterwards, but could Justin just be a figment of her imagination? She also has burn marks, true, but couldn't she have gotten them from other sources? We could have a Wizard of Oz scenario on our hands, where parts of the dream manifest in reality. 'There's no place like home' could instead be 'you can unlock any door if you only have the key'.
Nicodemus and the Owl are mysterious and surreal. Made for her to perhaps confront her timidness and seek help for it?
We do see the NIMH truck, but couldn't she have seen that outside the dream, which scared her and then made her think about why such a presence could be at the farm house? NIMH could've been a factor outside the dream to influence her thoughts inside.
The rats could've been a fable passed down through generations of her family. 'Auntie' Shrew seems to have believed in them.
Jeremy could also be a factor...Perhaps reminding her of her husband in someway? Maybe over-reaching, but it's possible. Perhaps in his silly nature and wanting to impress her.
So let's take everything in. A fable passed down through generations, a nefarious looking presence outside the farm house, stress of sick child and moving day woes, and a need to calm her fears. We could possibly have a dream on our hands. The ending being Mrs. Brisby telling her children the story.
So the Rats of NIMH didn't exist, what would that mean for the children? Would they seek Thorn Valley? What is Thorn Valley supposed to represent anyway? Heaven? Would the children tell the story to their next of kin and perhaps keep the cycle/dream of Thorn Valley going?
Have fun with this..or don't.