So that’s it, folks. We’ve come to the end of the road on season 3, and I have to say that I’ve got mixed feelings about last night’s finale. From the fake funeral in the beginning to the heartbreaking revelation of Gormogon’s apprentice at the end, much of the episode either rang false or felt a little too condensed for me. (We’ll reveal the killer’s name after the jump for those who actually haven’t watched the show yet. Get on that already.) Suffice it to say, for now, that to make me believe that ending, to wrap my head around that logic, it would have needed another episode or two to play out.

But let’s start with the fake out over Booth’s alleged death. I don’t think anyone really thought Booth was dead, despite Emily’s Deschanel’s superb acting, selling Brennan’s desire to stay within the cold embrace of her work to avoid the sadness of her Booth’s supposed demise. There was so much that could have been done with this if it were stretched out longer than three minutes. I concede that it may have taken the characters too far along their building-love path, but it seemed like a cheap trick to find out so quickly that after Booth was shot in the chest last week by stalker Pam that the FBI supposedly used that opportunity to fake his death and lure out another killer. And that the good doctor Sweets would use this as a chance to test Brennan’s feelings for her partner by not telling her that he was alive. Back in the lab, Brennan was rightly livid that she wasn’t told, and that anger led to last night’s finest scene for some: a naked Booth in the bathroom.

Now I won’t harp on the beer-can hat being a little incongruous (though, as one Bones-obsessed colleague of mine pointed out, there was a tray there that he could have used and a beer hat seemed too low-rent for him, even in the comfort of his bathroom) but from the Green Lantern comic book to the cigar to the vinyl record playing on an actual record player, that was a total guy-bath time. And let’s not forget the rubber ducky that shows up later. The scene might have been too light-hearted for some but a more serious scene, one in which Brennan didn’t actually gesture at his nether regions and ask if he wanted a towel, would also have brought them closer to the brink of consummating their sexual tension. And in our heart of hearts, we want them to put that off as long as possible.

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Speaking of putting things off for as long as possible — so Zack isour killer, huh? Not sure I did a double take, but I was perplexed bythe situation. I would love to be able to quote the first episode ofthe season, but wasn’t there something about the apprentice being awidow’s son? And didn’t Zack have a rather large, intact family (mother, father, siblings) that came to visit him at the lab during that Christmas episode in season 1? Itwas frustrating not hearing the scary logic that persuaded Zack, whowas not isolated or disenfranchised, to kill a man in the name of… what was it again?

I can’t help but keep thinking of how the everyone-is-a-suspectthing could have been stretched out longer. Hodgins and then Sweets assuspects could have been really intriguing. They were really sellingHodgins as the apprentice and T. J. Thyne was really creeping me outfor a bit. It was a bit of nice character development to have Sweetstake a stand against Booth’s threat to put him in handcuffs and arresthim. It took him from the sort of fawning man-crush he’d had on Booth,back to being an adult professional semi-authority figure. And even Camwas acting a bit suspicious, but that turned out to be just a sort ofjumpiness from knowing that someone at the Jeffersonian was the killer.Yet Tamara Taylor did an excellent job in the hospital-room scene whenshe found out that it was Zack. Her crestfallen face and dejection wereenough to transfer you from questioning the logic to feeling theemotion. Putting aside the exchange between Brennan and Zack, which wasjust a bit confusing, watching Zack’s friends gather around hisfavorite things (many of which they gave him), the shock and sadnesswere evident.

Still, among the many questions the episode left me with are these:

1) If Zack blew up his hands, who stole the skeleton?

2) If Gormogon did it, how did he get into the super-secure Jeffersonian? Wouldn’t that make him slightly more than a nobody?

In my interview with exec producer Hart Hanson, Hanson said he was expecting a “violent reaction” from fans. But here hefurther explains why they chose to make Zack the apprentice: “We hadgone pretty much as far as we could with that character. There’s anopportunity with that character to bring in a number of people. We’renot replacing him with a single character. We’re going have a bunch ofpeople coming in and out and that gives us a bunch of opportunities inthe lab for humor and stories.”

Hopefully this isn’t really a goodbye to Eric Millegan, who isactually a good friend of Hanson’s. “We’re looking for ways to have himback as a guest star from time to time. We love the guy,” says Hanson.”But you know, best laid plans. Eric’s a very talented guy and for allwe know will be starring on Broadway and that will be that. I wish thatfor him but not too much.”

It would be great to have Zack return next season, and as the squintsquad takes turns visiting him maybe we could get a better idea of whatreasoning Gormogon used to persuade him to commit murder.

Despite my many misgivings, I’m willing to give this episode a passon the strength of the first two seasons and most of this one. Thewriters and cast do such a good job with the relationship-building andhave come through so often that I can swallow the loss of Zack and hopethat they’ll pull off the next season, maybe even satisfying somequestions from this one.

So, how are you all feeling about this turn of events? How violentwas your reaction? Are you just shaking your fists or shutting thedoor behind you? Let us know if you’ll be back for the two-hourpremiere of season 4 on August 27. Have a good summer, guys.