The Secret of NIMH 2: Timmy to the Rescue (1998)

Timothy Brisby, now Timmy, leaves his family to train with the rats of NIMH in Thorn Valley. He meets Jenny, a mouse about the same age as he, who reveals her family are part of "The Lost Six" who did not escape NIMH. Timmy suspects his missing brother is also being held at NIMH and embarks on a rescue mission with Jenny while encountering old and new friends along the way.