If you mean...
WHY HIS CHARACTER WASN'T IN THE SHOW...
In the finale of Season 3 ( "The Pain in the Heart" ) it was found that Zach ( played by Eric Millegan) was the new apprentice of The Gormogon a cannibalistic serial killer. He was locked up in jail for the rest of his life.
or
WHY HE DIDN'T COME BACK...
He might have not wanted to be on Bones anymore.