Bones Shocker: Show Boss Breaks Down the "Devastating" Season Opener

[WARNING: The following story contains spoilers from Thursday's Season 10 premiere of Bones. Read at your own risk.]
Bones certainly kicked off its 10th season with a bang.
Although viewers spent the summer pondering how Brennan (Emily Deschanel) & Co. would free Booth (David Boreanaz) from jail and clear his name in the ever-growing FBI conspiracy, the show decided to throw an extra curveball by secretly killing off one of the show's own.

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That's right, once Booth was sprung from the slammer (thanks to a little blackmailing on Brennan's part), Booth quickly dug deeper into the powerful men he believed were pulling the strings of the conspiracy. But just as the team was closing in on their best lead, they were struck a crushing blow as one of the conspirators killed Sweets (John Francis Daley), who was attempting to serve a warrant to collect some damning evidence. Making matters worse, earlier in the episode it was revealed that Sweets and Daisy (Carla Gallo) had, um, reconciled while Booth was in prison and she is now pregnant with their child.Although Daley's exit from the show is connected with his desire to pursue writing and directing feature films (Daley is currently co-directing aVacation reboot in Atlanta), executive producer Stephen Nathan ultimately saw the loss of a cast member as an opportunity. Below, Nathan shares his thought process and outlines just how Sweets' death will impact the rest of the season. Plus: Find out why it might be possible to see Sweets again in the show's milestone 200th episode.How did this all come about? Was it purely a creative decision to shake up the storytelling, or was there a feeling that maybe John wanted to move on?
Stephen Nathan: Going in to Season 10, you really want to kick everything up a notch. Our intention, initially, was not the demise of Sweets. However, John's career as a writer and a director was really taking off, and he came to us and asked if he could leave to go and direct a film, which he's directing now. We were incredibly sad to lose him, which was really going to be the case because to have him come and go and come and go during the season would have been very disruptive for storytelling. When we realized that, we thought, "Wait a minute, what is the best way to use this unfortunate incident for us as an asset for the show?" The cliff-hanger from last season was leading up to a relatively complex story for Bones, and this seemed to be a very shocking and emotional way to deal with the story so it wasn't just a conspiracy story.

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It's certainly a bold way to open a season, especially one that already had high stakes built in from the cliff-hanger.
Nathan: This was so shocking. Cutting this episode, every time they got to that scene, I was just incredibly choked up because it's not only losing John, who we love, but it was losing a character we had grown to love on the show. I just felt what the other characters felt on the show. It was pretty devastating, but from an objective point of view, it was a very good thing for the show, and does inform the rest of the season. 
How so?
Nathan: Events like this change people in very fundamental ways, and everyone's life is altered as you'll see in the second episode. The second episode actually deals with the funeral which, needless to say, is a very non-traditional event. But [everyone] deals with what this means for them and what Sweets means to them because Sweets is not gone in a very fundamental way. Daisy is pregnant. Life goes on. The trauma that has been brought upon them by Sweets' demise is not something that can go away easily.
Would you describe this as a darker season as a result?
Nathan: The show will get its footing again. The second episode, we'll see a conclusion of sorts of this first story that we've been dealing with from the end of last season, and our characters will be heading back on the Bones bandwagon. We're not forsaking what makes Bones, Bones, which is all the humor, the romance, the oddities of our cases and the skewed comic nature of our show. That's a groove we're going to get back into, but that doesn't mean it doesn't come with baggage now.

Does Booth feel responsible since he insisted on charging forward with the case that ultimately leads to Sweets' death?
Nathan: Yes. All of that will be dealt with in the second episode. The second episode really  is a continuation of the first episode, and all of those issues will be confronted and dealt with.

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And do those emotions just compound the feelings he has about how much the FBI has betrayed him?
Nathan:  He will be moving forward with that. That's not something he can get rid of in one episode. He has to learn how to trust the organization that he devoted his life to again, and he has to learn how to trust a new colleague at the FBI, which is Aubrey. Aubrey is now there —  not as a replacement for Sweets because his job description is much, much different —and he's somebody that Booth has to learn how to work with and also someone he has to learn how to trust. Trust is the issue that he will be wrestling with for a little bit. Then we also have all the other balls that are up in the air, one of them being Daisy and her pregnancy.
Daisy asked Booth to be the godfather of this child in the premiere. Obviously, that's potentially a much bigger role that he will have to play now that his father is gone. Will Booth wrestle with that?
Nathan: It certainly can't happen right away, but when we deal with the baby, it's going to mean an awful lot for everybody. Daisy's alone and her family is our family.
In typical Brennan fashion, she's able to stifle the emotion and stay focused on how important is to solve Sweets murder. Will bottling that emotion up be good for her?
Nathan: Brennan handles things in her own way, clearly. It's difficult for everybody, but the devil and angel that Brennan lives with is her ability to compartmentalize and deal with what would be emotionally devastating circumstances for another person in a very practical and an objective manner. That becomes an angel for her in that situation because she has a strength that allows everyone to move forward.

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Will there be a time jump between Episodes 2 and 3 that help with the tonal shift?
Nathan: Yes, probably. It's not stated. We don't say, "two months later," or anything like that. It's not that much more in the future. Our characters are strong. They've lived through massive trauma before and so they have a strength to meet these challenges, and they have not lost that. The second episode case-wise is a very traditional Bones, but the emotional life of our characters carries over from the first episode. There are issues that we're dealing with, but we're moving forward. We don't want to mire the show in a darkness.
You also said the second episode brings this larger story to a conclusion of sorts. Is this FBI conspiracy something you want to touch back on throughout the year?
Nathan: It might. It still remains to be seen. If you have a far-reaching conspiracy, it's like having the exterminator come to your house to get rid of the ants. He gets rid of most of them, but there still might be a few ants around when he leaves.
What can you tell us about this season's big 200th episode?
Nathan: It's going to involve as many characters as we can reassemble. It's going to be a very unique style piece, unlike anything we've done before. [It's] a real love letter to the fans. [We'll be] seeing all of our characters in a new way, but somehow it's still our characters. It's not an alternate reality, but it is going to be unique.
By opening up the season with such a bang, what do you think it says about the rest of what this season will be?
Nathan: There's no reason to hold back. Television being what it is now, I think every week you want to come out with guns blazing. So, we want to mix it up as much as we can. We just really want to keep exploring these rich characters. ... Every year, they add more to their lives and to their complexity, and we just want to keep exploiting them as much as possible. That means having more extreme situations, and more extreme emotional lives for these people.
Bones airs Thursdays at 8/7c on Fox. What did you think of the premiere? Will you miss Sweets?

Watch the video below to see the cast members' reaction: