Bones showrunner on how series finale 'redefined' Brennan

Warning: This story contains spoilers from the series finale of Bones.

Booth and Brennan have finally walked off into the sunset—well, the night.

Bones' series finale left the show's core characters in a good place: Brennan (Emily Deschanel) recovered from the brain trauma she sustained in the Jeffersonian bombing, Booth (David Boreanaz) took down the bomber, Cam (Tamara Taylor) and Arastoo (Pej Vahdat) are adopting three boys, and Hodgins (TJ Thyne) and Angela (Michaela Conlin) are having another baby. And since Cam has named Hodgins her interim replacement while she gets the kids settled in, Hodgins is the new king of the lab.

But the road to this happy ending wasn't always smooth, as Brennan's head injury affected her ability to do her job and gave her a serious identity crisis. Showrunner Michael Peterson, who wrote the episode with co-showrunner Jonathan Collier and executive producer Karine Rosenthal, talked to EW about wrapping up Brennan's story, crafting the end of the show's ongoing 4:47 mystery, and which member of the team might not be long for the Jeffersonian. (Head here for star Emily Deschanel's thoughts on Bones' final hour.)

ENTERTAINMENT WEEKLY: Tell me about the idea behind giving Brennan this brain injury and what you wanted to say with that story.

MICHAEL PETERSON: Stephen [Nathan, former showrunner, who plotted the story] was just fantastic in coming up with, especially, this personal arc of Brennan's in the final episode. What we wanted to do this season is really challenge who Brennan is. When we meet her in the pilot way back when, she's somebody who's struggling to connect with other people, struggling to figure out who she is. Her parents went missing. We see ourselves so much through the eyes of our parents, so that was her quest for so many years to figure out what happened to them. Ultimately she finds out, and she realizes that she's not even living by her actual name.

It's been this constant quest of hers to figure out who she is, and we wanted to make the challenge that much harder in this final year. Her father dies. She's worked so hard to get there [with him]; now he's gone. Who is she? Who is her family? And this last episode is this final hurdle she has to overcome. She's helped to redefine herself through this family that she's formed at the Jeffersonian and with Booth and with the kids, but in this final episode, we take away that one thing that she has always defined herself by, and that's her intelligence. She's questioning, you know, where's my place in the world without this? And Booth helps her to see what she looks like through his eyes and makes sure she knows how worthy she is as a person beyond her intelligence.

Were you worried at all about going so far in the other direction that it might come across as dismissing her intelligence or her pride in her intelligence?

That's a very fair question, and I think at the end of the day, that's why we didn't take it away. There's nothing wrong with her intelligence at all. It's a wonderful virtue. But I think her arc as a character is about defining herself and seeing herself in a more rounded sort of way, so we didn't want to take that away permanently, but just to get her to a place where she realizes that she is so much more than just her IQ. She's a more well-rounded person than when we first met her. She's taken down these barriers and opened herself up, and we wanted to acknowledge that.

You told me after Hodgins was paralyzed that you always try to aim toward a happy ending eventually on this show. Was that always the guiding principle for this finale, or did you ever consider going darker?

There were lots of considerations. There was consideration of letting Hodgins walk again: Is that the lightness we need to run towards? But it was kind of like the Eric Millegan decision to not just have [Zack] free and out of prison; it didn't feel real. And I think it's a very important reminder: Just because we have our struggles and we have a disability or whatever else, it doesn't mean life isn't joyful. It can mean quite the opposite. You gain new perspective… So I don't think we ever considered going much darker. [We considered going] lighter.

Is there any chance Cam is not going to come back to the Jeffersonian after her six months away?

Yeah, I think that's very much a real chance. I think she and Arastoo will make the tough choices as they look at their careers together. But you know, that's life. People do move on, but it doesn't mean that friendships die out.

Angela, on the other hand, has always talked about leaving. What was the thought process behind keeping her settled at the Jeffersonian?

First of all, it just felt like territory that had been mined, to be honest. And she's also changed so much. She's not just wanting to go off and be in Paris and be this famous artist. Her priorities have changed as a mom and as a friend and everything else. She's already made that conscious choice in her mind that things aren't going to work out exactly as you want it, and that's good. I think the strongest people have the ability to change who they are, and they change their ambitions as they go along, and Angela is definitely one of those people. She's not going to just hold on to an old dream. She's going to make new dreams every single day.

There were so many references to past years in this final episode and final season. Did the cast have any input in the callbacks?

The Mulder/Scully line that Booth alludes to in [the finale] was absolutely David. He was like, "Yep, we gotta do it, we gotta do it." And there were moments when we were like, "We want to be humble, we don't want to compare," and he's like, "It's a joke from the pilot. You gotta do it." And I think at the end of the day, he was right. We certainly didn't want to throw any shade on anybody else. But I think it worked at the end of the day, and it's funny for those fans who remember the callback to that very first episode.

We got the final piece in the 4:47 puzzle. How did you settle on the meaning behind it?

There were a lot of arguments and discussions. Everybody has a different way of looking at it. [Series creator] Hart [Hanson] had a very erudite and literal way of doing it which was too hard for us to do. We were like, "If you want to come in and write it, we'll take your pages, absolutely." But we tried to wrap it up as best as we could. Everything else we've teased with 4:47, I would call omens leading up to this moment. It's just this reminder of 4:47 being a key in their lives, and for me, it's that moment when everything redefines itself. Brennan goes through this struggle, and she comes out the other side a changed person. She is able to see herself in a different light.

Same with Booth—he is finally coming over this guilt that he has been carrying around for forever: these lives that he has taken, and the key life that he has regretted the most is having to shoot this person in front of their child. In this action and in their survival, they are changed. Booth is finally able to absolve himself from his guilt because Brennan talks him through it. Same with Booth—he's able to help Brennan redefine herself and see that she is more than her intelligence. 4:47 is that moment when their life changes one more time. They're that much closer to each other, and they're able to walk off into—not the sunset, walk into the night, in our show. And you know that they're going to be okay.

Any chance I can get you to say anything about Hart's idea?

He's just too smart for me to be able to explain. It had something to do with Brennan just being the exceptional woman that she is. But he really could say it so much better.

At the end of the day, what do you hope people take from Bones?

I think that whatever each individual takes from it is really up to them. To me, it was always a show that was about hope… Hart is one of these guys who's just filled with great hope, and the characters and the action of the show are infused with that. Even just the characters—it's amazing to me that we have these three lead women in science who are very different but who are pointing to the future where there is more equality, where these fields are open to anybody. There's just something about the show that has always been very hopeful.

And I want people to feel that even as the show ends. We see Booth and Brennan walking off, and they're changed people, but you want to have that feeling that yes, they're still going to be out there, and they're still going to be solving cases and making the world a better place, even if you're not going to see them anymore. They're still joking and laughing in the car, having their differences and having those playful fights they have. You really hope that's still going on when you don't see it. It's certainly bittersweet not to be able to see them again, but just to feel that they're all in a good place and they're going to be okay. And you as a viewer are going to be okay, too.