As a Moments subpage, all spoilers are unmarked as per policy. You Have Been Warned.
- Martin's torture and Mind Rape while at NIMH. Also crosses over into Nightmare Fuel.
- The fact that Mrs. Brisby's contributions from the first film have been almost completely ignored.
- Timmy remarking that he never knew his father, and yet is expected to live up to his legacy.
- Mrs. Brisby's farewell to Timmy, knowing it would be years before she'd see him again.
- The scene where Timmy finds out Martin was captured by NIMH. When asking Jenny how she knew how to reach Thorn Valley, she tells him a mouse at NIMH told her to go "South by South by South", which, as Timmy remembers, was what Martin had said to Jeremy at the beginning of the film. Jenny then says that Martin was the name of the mouse who told her the directions, and asks Timmy how he knew that. That's when Timmy reveals to Jenny that not only is Martin his brother, but he had received a letter from his mother, telling him Martin had disappeared. Timmy is naturally horrified when Jenny confirms that Martin is at NIMH.
- Also a bit of Fridge Tear Jerker; one can only imagine what poor Mrs. Brisby was feeling that day, especially when you hear Timmy mention that she had no idea what happened to Martin. To her, it probably felt like she was reliving the day Jonathan died all over again. Because if you remember in the original film, until she met the rats of NIMH, she never really knew what had happened to her husband, all she knew was that he never came home.
- Timmy's Despair Event Horizon; queue "All I Have Is Gone"; it's even more solemn in the end credits.
