Danny, his friends, the Berenstain Bears, Team Lightyear, Zack and Ivy, Bernard and Bianca went on a journey to meet Mrs. Brisby, who lost her husband and had kids. On this adventure in the Rose Bush, they meet Justin, who told Mrs. Brisby about NIMH coming to the farm, and face-to-face with the evil Jenner, to save Mrs. Brisby's family.
- The storyline continues from Danny and the Secret of NIMH 2: Timmy to the Rescue.
- Mrs. Brisby is revealed to be Timothy's aunt. (Timothy Q. Mouse, actually, and it says that so viewers won't think this claims that she is Timmy Brisby's aunt when she's really his mother.)
- Jeremy is revealed to be the Crows' cousin.