I didn't get into the season-long Gormogon killer arc, but that may be because the season was interrupted. More interesting to me, the finale started with everyone except Brennan planning to attend Booth's funeral. As always, Brennan/Deschanel manages to sound spoiled and utterly practical at the same time. I didn't know where Booth was or what shape he was in until the camera caught him in uniform. I think they could have played the possibility of Booth's death for even more drama (He's shot badly enough to go into shock, and two weeks later he's fully mobile with only a patch to show for it?) but anyway, episode writers Hart Hanson and Stephen Nathan hinted at and hid the identity of Gormogon's apprentice well. As often as it's been done, you don't expect the character who takes the hardest hit near the beginning to be the killer. In the end, the apprentice showed the typical traits of a weak personality seduced by a stronger one. Still, I wouldn't have believed the character could be seduced.
UPDATE - SPOILER (5/21/08): In an interview with TV Guide, Eric Millegan revealed he had no plans to leave Bones; Zack's turning killer was purely a creative decision to make a more dramatic end of the season.