Secret of NIMHEdit
Before the events of the movie, Jonathan is killed and eaten by the cat Dragon in an attempt to drug him. His wife, Mrs. Brisby is never informed of this until she meets Nicodemus who tells her all about NIMH and the rats' escape. He is seen briefly through Nicodemus' magic sphere helping Mr.Ages through an air vent. Presumably at NIMH. After this, he is only mentioned and never seen again.
Secret of NIMH 2: Timmy to The RescueEdit
Although never seen in person, he is mentioned in the sequel by Mrs. Brisby and Justin. Additionally, a statue with his name engraved is seen multiple times. The engraving is later changed to: "Jonathan Brisby and son" with an attachment showing Timothy next to him.