Does anyone know what actually happened to brenden? I noticed that after awhile, he wasn't on the show anymore and was just wondering why or how they cut him out?

This has been discussed a lot already, but Brendan's disappearance on the show is still mystery. My guess is, please don't quote me, that Josh Byrne, the actor who played Brendan, probably left the show because his character didn't get enough screen time.

Looking into Step by Step, when the show moved to CBS Brendan was no longer with the show(the last season). Which backs up TVTOME notes which state that after the move to CBS Josh Byrne (Brendan) was dropped from the cast. Which means probably both CBS and the show didnt see a need for his character.