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I wore mine out, lol, but there were scenes that they changed from the movie (to make it kid-friendly, I guess) that just seemed so out of character and just made me scratch my head: Mrs. Brisby calling out "Yoo-Hoo" to Mr. Ages: Very out of character. When she loses Timmy's medicine: "Oh, boo-hoo-hoo! I've lost Timmy's medicine! Oh, boo-hoo-hoo!" (You almost expect her to say, "R'ally, Ah have!")
Nicodemus concluding the story of their escape from NIMH, saying that "all the mice except Jonathan and Mr. Ages were (lost in the air ducts)". He doesn't tell how Jonathan opened the locked door, or was later killed during one of his cat-drugging missions.
The fight: What the H-E-double hockey sticks happens to Sullivan? He offers Justin his sword, Jenner knocks it out of his hand/paw and accuses him of being a traitor. Does he kill him off-screen--er, off-panel?
Jenner's defeat: Justin, now with Sullivan's sword, wounds Jenner and sends him tumbling into the water. (Jenner (screaming): "Aaa-hhh! I--I'm WOUNDED!" (Clambers out of the water, shaking his fist and cursing) "Go on! Go to Thorn Valley and starve! You haven't heard the last of me!" Justin: "You're through, Jenner!" (Which means he'll be left behind for the people from NIMH to deal with the following morning?)