Question: What happened to the orphans at the end of Annie? Did they get adopted with Annie or are they still staying at the orphanage?
Answer: They are no longer at the orphanage since Miss Hannigan reformed and became a schoolteacher. So they are all adopted with Annie by "Daddy" Warbucks.
Answer: They're still staying at the orphanage, but it seems Mr. Warbucks is helping to fund them and Miss Hannigan has had a change of heart, so it's not so grim.
Answer: Annie and Molly both get adopted by Oliver Warbucks and become sisters ages 10 and 6 and live with the male family dog, Sandy and Oliver marries Grace Farrell and Grace becomes Annie and Molly's mom.
Answer: 10 year old Annie and six year old Molly and another orphan named Chloe get adopted by Oliver Warbucks and have the male family dog, Sandy and Oliver marries Grace Farrell and Grace becomes the girls' new mom.
Question: How did they make Kirk Douglas have a peg leg? How was he able to walk that way?
Answer: This movie predates the more advanced CGI that would be used these days. In older films, actors portraying an amputee would have their leg (or arm) bent back and strapped to their body. A prosthetic peg leg would be attacked to the lower appendage. The actors were also filmed from strategic vantage points so the bent part of the limb didn't show. When Douglas is seen driving a wagon, the seat was probably constructed so that his lower leg fit into a hidden compartment and the peg leg was attached on top to be visible. Douglas also wore rather baggy pants, and that would help conceal his bent leg.
Question: When Jen looks at the shard, he sees in image of a Skeksis striking the crystal, but why when the beings of light appear, do they say that they were the ones responsible for shattering it?
Answer: The skeksis and the beings of light are the same, each being a different side (good and bad) therefore it was there evil side (the skeksis) that struck the crystal.
Question: If Jonathan and Mr. Ages were the only mice to survive the escape from NIMH, then where did all the other intelligent mice come from? Did one or both of them father a new generation of intelligent mice? Mrs. Brisby's marriage to Jonathan makes this all a little confusing.
Answer: Mrs. Brisby tells Nicodemus that Jonathan had been teaching her to read and her children as well. The children were better at reading that she was but that might be something that they inherited from their father. I think Mr. Ages was also able to read so that makes him intelligent as well. Remember the injections that the mice and rats were given also gave them the ability to read.
Answer: What other intelligent mice? I have watched the movie many times and I don't remember seeing any other intelligent mice. The mice that tried to escape with the rats were sucked down the ventilation shafts, so we don't know what happened to them.
Well, Mrs. Brisby for one, and by extension, her children. She wasn't part of the experiments at NIMH, so why does she possess human intelligence like Jonathan and Mr. Ages? Similarly, why do Jeremy, Auntie Shrew and the Great Owl have human-like intellect as well?
Answer: Molly gets adopted by Warbucks and becomes Annie's sister and the other orphans get adopted by other families while a reformed Miss Hannigan becomes a schoolteacher.