Bones (the TV Show)

A friend of mine told me about Bones and so I watched the first 3 seasons on DVD over the past few weeks. I really liked the show until I got to the last episode of Season 3, "The Pain in the Heart"

First, the whole opening with Booth's funeral and him faking his death to catch some bad guy we'd never seen before? I wanted to see more of what happened between the end of the last episode where he got shot and him "dying" - wouldn't Brennan have been with him at the hospital? How long was he in the hospital before he "died" - how bad was the actual gun shot? He seemed pretty well healed.

Then, with Zach turning out to be Gormagon's apprentice. That in and of itself didn't bother me too much, but what did bother me was, since Zach blew off his hands, who stole the silver skeleton? In a previous episode where Booth is chasing the person who initially came after the politician we see that person take the motorcycle helmet off and its a woman - not Zach and not the creepy guy the find / kill at the end. So what about her? And the whole way that episode ended with Zach "knowing" how to find the guy, etc. I found very hard to believe although I can understand they just wanted to wrap up that story line. However, another question I have is - why did Hodgins pump up Zachs pain meds when Zach was, in theory, about to reveal some clue? I know it was to make Hodgins look guilty at the time but since he wasn't the bad guy, why did Hodgins do it? Are they trying to set up that Hodgins was also the Gormagon's apprentice - he stole the skeleton and Zach was going to give him up? Is Zach covering for Hodgins who really is the apprentice?

I'm really torn about the show and whether I should continue watching it. Does the show recover from this episode? Any thoughts would be appreciated.