Emily Deschanel explains the season finale of “Bones”

I participated in a conference call with Emily Deschanel last week, and the question on everyone’s minds was the question that’s been on everyone’s minds since the Bones season finale was spoiled by executive producer Hart Hanson months ago.

(If you don’t know about the spoiler to which I am referring, and do not wish to know the about the spoiler to which I am referring, close the window! Hurry! I’m activating a SPOILER ALERT for the rest of this post.)

In case you missed it, or just like seeing it spelled out again, Booth and Brennan are going to end up in the sack on the season finale of Bones. WHOTHEWHATNOW? was the initial response to the leaked information, but after processing it properly, fans are now able to calmly ask, “Who the what now?” Or more precisely, “How?”

Short story: After four solid seasons of protesting motherhood, Dr. Brennan has decided raising a child may be one of the most selfless things she can do with her life. And the perfect candidate to father Baby Bones? Agent Booth, obviously.

Fan response has ranged from ecstasy to dread upon finding out that the two are going to finally sleep together. Will it ruin their chemistry? Will it be that familiar kiss of death that has offed so many of TV’s other great pairings? Does it even count as “getting together” if they are really only getting it on in the interest of procreation?

“I’m glad we waited this long. I don’t think we should have waited longer,” Deschanel told us. “I think it was a matter of time, and figuring out the right way so it doesn’t ruin everything for the show. I’m happy about the way it turned out.”

Of course, knowing the end result and watching a story unfold are two completely different things. “It should be surprising. The way it happens will be surprising,” Deschanel promised.

She said the main question on everyone’s mind has been that whole “whothewhatnow” thing, but she teased that the way it happens will create an entirely new line of questions.

There has been much discussion about the sudden clang in Dr. Brennan’s biological clock. Isn’t it a bit out of character for someone so hyper-rational to decide she wants to have a baby and just BAM! try to get pregnant? Deschanel addressed that too.

“You know, I like this decision […] One thing I love about Hart’s characters from the beginning is that they have contradictions. That’s one thing I originally loved about the script for Bones.

And while she liked Brennan’s bold position of being one of the only characters on television to say she didn’t want children, she was happy with the way the storyline unfolded: “You see a softer side. You see her in a completely different situation, a different environment, a different character. Definitely a different side you haven’t seen before.”

Temperance Brennan is one of the most dynamic female characters on television right now. This season, especially, Bones writers have begun peeling back her layers, allowing her to explore her emotions, to question the way she relates to people, to see how her past conditioned her present.

In the recent episode “Mayhem on a Cross,” Brennan offers Dr. Sweets a look at her emotional scarring, hoping to help ease the physical scars he received at the hands of abusive parents. She explains that when she was in foster care, her parents locked her in a trunk for two days because she broke a plate.

“They warned me it would happen,” Brennan says, trying to add reason to the unreasonable, and finding her voice cracking anyway. “But the water was so hot, and the plate was so slippery. I still don’t think it was fair even though they gave me fair warning. The water was so hot.”

I’m not sure Brennan is softening, but she’s certainly opening up, and Emily Deschanel is playing it brilliantly.

All the talk of relationships and motherhood might make you worry about the fate of our favorite forensic anthropologist — if it weren’t for the fact that Brennan looks at marriage and kids like this, “Just because I don’t want to take part in a meaningless ritual doesn’t mean that I’m not a warm and affectionate person. There are even some children who have taken to me.”

Here are a couple of other tidbits about the last three episodes of the season:

Zack will be back for the season finale. (“Aw, it’s wonderful to have [Eric Millegan]) back. I enjoy his company so much.”)

Motley Crue will be in the finale too, playing at The Jeffersonian. (“I don’t want to reveal too much, but Booth and Brennan know them, actually.”)

Family Guy‘s Stewie Griffin is going to pop up in one of the last three episodes. (“It’s gonna be a little bit like a Mary Poppins kind of thing, but so much more modern and cool.”)

Bones will be back to its regular time, 8:00 EST on Fox. Are you stoked about the last three episodes of the season?

Editor’s note: please don’t reveal spoilers in the subject lines of your comments. Thanks!