Credit: Ray Mickshaw/FOX

SPOILER ALERT! If you haven’t yet watched the Bones season finale — or been spoiled by a Canadian fan who saw it a day before it aired in the U.S. — then stop reading now. Executive producer Stephen Nathan phoned EW after the East Coast airing to talk about the real change in the game…

ENTERTAINMENT WEEKLY: So I just spent five minutes yelling “WHAT?” at my TV — in a good way. I can’t believe Brennan is pregnant. Some fans are worried that because Angela used the word “dream” in conversation with Brennan, Brennan’s conversation with Booth was just a dream. But she really is pregnant, correct?

STEPHEN NATHAN: Absolutely. This is not a dream.

Would this be happening now in the story if Emily Deschanel hadn’t become pregnant in real life?

Yes. This was something that we had been discussing even before Emily found out she was pregnant. It’s very difficult to find a way to deal with two characters who everybody knows should be together without embracing what everybody calls the Moonlighting curse. We had to find a way to keep the integrity of those characters intact, and yet move them along because you can only wait so long. So we wanted to avoid that part of the relationship where you first get together and the fresh glow of love, and you’re sharing dessert, and you’re overly polite. We didn’t want to do that. Booth and Brennan have disagreed about fundamentally everything — except each other — for six years. That will continue. Their characters will remain the same: Booth and Brennan will have completely different ways of dealing with the pregnancy, completely different ways of dealing with where their life goes from here. Booth is the marrying kind as we know, and Brennan is not. Where are they gonna live? How are they gonna raise the child? How are they gonna continue to catch murderers together when they have a baby hanging around? So all of these issues will be dealt with in the way that they’re always dealt with — from opposite sides. The ultimate pragmatist meets this romantic who has faith that everything will be worked out as long as you look at it the right way. These are issues that won’t die. We hopefully have found a way to continue what everyone loves about Bones while really kicking it up a notch and adding a whole new set of complications now that these two people actually find themselves together.

Do you anticipate a time jump when the show returns in the fall?

It’s not gonna be two weeks later. We’ll see them a little bit further along. Exactly how far along remains to be seen. We’re working that out now.

What was the time jump between Nigel-Murray’s death last week and this week when she told Booth that she was pregnant?

It’s probably at least a month.

Did they sleep together just that once, or have they been sleeping together since that night?

I think that’s up to every viewer. I have my little feeling about it, but I don’t want to impose my opinion on that on anyone.

After last week’s episode aired, some fans felt cheated that if there was a real love scene, we didn’t get to see it. Will we ever get to see that moment, or will we just move forward?

Well, we’ll now see them as a couple — whatever a couple means to Booth and Brennan. [Laughs] It will be that unique couple. It won’t be what you expect.

Another question fans had is the significance of 4:47, which we’ve seen on clocks in the season 4 finale, the season 5 finale, and last week’s episode.

It’s just a little consistency that we try to string through the series, just [to mark] important moments: 4:47 was when they slept together in the alternate reality, and 4:47 was when she walked into the bedroom last week. So, you know, I guess it’s our little smoke monster. [Laughs] It’s Bones‘ stab at being Lost.

Moving on to Angela and Hodgins: watching the finale, I was like, “She really should have been training someone to take over for her during her maternity leave.” But if you do that little time jump, you can skip over that as well.

They’ll be back to work. Bones is still Bones. We’re still gonna have gruesome murders and find the killer. That’s still always the main thrust of the show. We’ll follow their lives and follow the progression of relationships, but that’s always gonna be the backdrop against killing people. [Laughs] The babies will definitely factor in the show. Every week? I can’t imagine. But it will be a part of their lives. We’ve known these people for six years. We’ve seen them grow. This is what happens when people this age get married. They have children and their lives progress and evolve, and we’ll see a part of that while we’re, you know, tearing the flesh off of a horrendously decomposed body.

I know The Finder will sub for Bones at some point next season to allow for Emily’s maternity leave. Do you know how many Bones episodes we’ll get next season?

We’re gonna do as many episodes of Bones as we possibly can. There are realities that we’re dealing with: Emily’s going to be having her baby and taking some time off to enjoy that moment, as she should. And then when she comes back, we’ll do as many episodes as we possibly can. We have a number we hope to achieve, but we just don’t know. Those things are a bit up in the air.

Last question: What would you like to say to fans who are weary of the show bringing a baby into the Booth and Brennan dynamic?

It’s not like Alf has come into their lives, it’s something real. We want that to affect the show, but it’s not gonna be a show about having babies. It’s not Parenthood. I’m sure there are gonna be some viewers who are upset. “Oh, the baby’s gonna do this and do that.” A lot of viewers always make up their mind on how we’re gonna ruin the show before it happens. [Laughs] And hopefully we will disappoint those viewers. And the viewers who have faith that we’ll be able to take the show into new territory well, we hope we won’t disappoint them. We’re very, very excited about being able to do the show that we love doing, but do it with fresh eyes.

Read more: