- The tractor scene is very unnerving, with the heavily rotoscoped tractor slowly creeping through the field and deliberately clashing with the rest of the film's Disneyesque style. The fact that the whole thing takes place from the perspective of the animals, with The Shrew running through the field screaming "THE PLOW IS HERE!!" turns a simple farming job into Armageddon.
- Jenner, for his actions, demeanor, and utter ruthlessness in getting what he wants. In the scene where he tells Sullivan about his plan to kill Nicodemus, he tells about how the Brisby house will "crush his bones" while pulling off a Nightmare Face. When asked what to do about Justin, Jenner's response is an echoing "Leave him to me... to me... to me..."
- The Great Owl, from the perspective of a little field mouse like Mrs. Brisby, really is a Great Wyrm (minus the firebreathing). His opening act is messily crushing a spider right next to Mrs. Brisby and it gets worse from there. But perhaps the most shiver-inducing scene is before we ever see him. When Mrs. Brisby calls into the seemingly bottomless dark hole that is his lair, this drifts up almost lazily from within:
Step inside my house.
- The spider that he crushes is even more frightening.
- Dragon, the farmer's massive cat. It's much worse than it sounds.
- He was really scary! Especially when he was chasing Ms Brisby and the close ups of his nightmare face!
- Mrs. Brisby's encounter with Brutus, who's seemingly hellbent on outright killing the frightened and defenseless mouse when she comes to seek out Nicodemus, and she just barely escapes his rampage.
- His blank, expressionless eyes and dark visage make it all the more terrifying.
- Not to mention his chosen weapon, an electrified spear.
- The sequence describing the rats' experience at NIMH. Starts off with sad imagery of animals in too-small cages, then they show a rat being injected with God-knows-what and the Disney Acid Sequence begins.
- The rats being shown bending over and clutching their red-glowing abdomens as the drugs take effect, with the rising heartbeat sound, is horrifically visceral.
- The scene where most of the mice (except Jonathan and Mr. Ages) are blown away in the air shaft during the escape.
- The expression on Jenner's face as he is killed by the knife Sullivan threw into his back.
- The thought of four children trapped with their house sinking into the mud is unsettling in itself. Even more so if you put yourself in Mrs. Brisby's situation.
Cynthia: What's all that black stuff?
- Speaking of which, just where was Timmy when all of this was happening? Timmy was still in bed.
- The mud itself is even more scary.