David Boreanaz David Boreanaz

[WARNING: The following story contains spoilers from the Season 9 finale of Bones. Read at your own risk.]

For years, Bones season finales posed a number of threats to the future of Booth and Brennan's personal relationship. However, on Monday's Season 9 finale, it was the future of the now-married crime-solving duo's professional partnership that was in danger.

Bones star: The finale "changes everything" for Booth and Brennan

While Booth (David Boreanaz

) was preparing to be confirmed for his new FBI role in Germany by a Congressional subcommittee, he was contacted by a conspiracy blogger who claimed that he could connect the McNamaras — aka the family of the Ghost Killer — to someone in the FBI. Unfortunately, Before Booth could question the blogger, he was found dead in his torched mobile home.However, Brennan (Emily Deschanel) and her team at the Jeffersonian were able to access the dead blogger's files (via a nipple ring!), which included a ton of photos and documents someone at the FBI was using to blackmail others to do his or her bidding. Not knowing who inside the FBI he could trust, Booth kept digging in secret — or so he thought. While Booth was testifying at the Congressional hearing, a formerly supportive Congressman Hadley revealed classified information about Booth killing a U.S. citizen in Pakistan and effectively squashed Booth's chances at being promoted.Realizing that the conspirator(s) had blackmailed Hadley, Booth told the congressman he had all the files, which Booth hoped would lure his enemies to attack. After clearing Brennan and Christine out of the house, Booth prepared an arsenal of guns and booby-trapped the house with C4 and other explosives while he waited for the conspirator's Delta Force henchmen to come. And come they did. After a protracted firefight, Booth took a bullet to the stomach and would have likely been a goner if Brennan didn't return to the house to help Booth finish off the men.

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Booth was rushed to the hospital, and although his prognosis temporarily looked grim, he pulled through. However, in the episode's closing moments, Deputy Director Stark (Sterling Macer Jr.) stormed into Booth's hospital room and arrested him for the murder of three FBI agents (aka the Delta Force soldiers). Brennan screamed in protest, which forced agents to also drag her away to be questioned.So, is Booth's career at the FBI toast now that he's headed off to jail? Or can Brennan & Co. save the day? And who is pulling the strings of this conspiracy? TVGuide.com took all our burning questions to executive producer Stephan Nathan.As you were building this season, what did you want to accomplish with this finale?
Stephen Nathan: We wanted Booth and Brennan and the audience hanging in sort of a rage of uncertainty. We wanted to put them in a situation that they haven't really been in before. They've always been able to trust the FBI [and] the organizations they worked for. Rather than go with a traditional serial killer format, we wanted to try and take the show in another direction, at least temporarily, to have Booth and Brennan take on some force that is far larger, far more vague than anything they've dealt with before. We caught the Ghost Killer, but there's still a ghost out there, some kind of adversary that still remains unseen and unidentifiable at the end of this season.And that unseen force really does a number on Booth and Brennan in those final moments.
 We're going into Season 10 really dealing with the consequences of this finale. Booth is in handcuffs, Brennan has been taken into custody for questioning, and has been dragged away from Booth. The pain of their separation as well as the uncertainty of how this is going to play out is really how we wanted to leave the audience because it does a few things for us. It confirms this relationship which everybody has invested in and it solidifies that even more. Season 10 will start with all of this unresolved baggage, but with the determination of Brennan and Booth and the squints to draw this very painful and ugly chapter to a close.  

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Do you anticipate a time jump between seasons?
: Traditionally, the time jumps have been somewhat in real time. We're going to be treating this in the same way. Booth will have been languishing and suffering in the situation caused by this finale, and everyone is going to have to try to save Booth because the forces seem to be coming down on him.

So, Booth will still be in custody?
Nathan: We will open Season 10 with Booth in custody. Booth will be in jail awaiting trial. As always happens from the time you're incarcerated to the time your trial starts can be quite a long time. All I can say is it is not a good situation for a law enforcement officer to be incarcerated with criminals.


How much fight does Booth have left? Will he take this betrayal by his own agency hard?

Nathan: He does feel unmoored. He doesn't know who to trust, but Booth is a patriot. Booth has fought for his country, Booth has believed in the institutions of the country. There is no more heinous betrayal in Booth's mind than the corruption of an institution that has been set up for the public good. ... At the same time, Booth is an optimist against all odds, and that's the only way he can be the soldier he was. Even though you're pinned down against all odds as he was in the finale, he believes that he can win. There is a tremendous amount of faith and belief that what's right will triumph and that has been the guiding light of Booth's life. That will not desert him.

Speaking of Booth's optimism, he was fairly certain he could take out those Delta Force guys all by himself. But Brennan saved the day. 
Nathan: She came back and stood by Booth and did what she had to do for not only her husband and the person she loves, but also for her partner. I think if they had to do it over again it would play out in exactly the same way.

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There are three bodies at Booth and Brennan's house. Could Brennan use those men's identities to continue the search for the leader of this conspiracy?
Nathan: Booth was arrested for killing three FBI agents. How did [these men] get accredited? Are those credentials legitimate? What did Brennan take from the scene? What is Brennan going to use to close in on this? If we're dealing with somebody who will keep himself insulated from recognition, how do they get to that person? That's what we'll be doing in the beginning of Season 10.

Deputy Director Stark orders Booth's arrest. Should we assume he is in on the conspiracy if not the very one orchestrating it?
Nathan: That's all up to the audience at this point. That's not something that I can say. He might be a perfectly lovely guy, or he could be evil. He could be a victim himself, or he could be the mastermind. At this point, we just wanted to leave the audience hanging in a rage of uncertainty.

As you mentioned, you have spread out serial killer cases over several episodes, sometimes even seasons. Do you see this conspiracy playing out for a good while yet?
Nathan: This is going to be like peeling back the layers of an onion. We will resolve everything we need to resolve to get the show back on track [in Season 10], but that doesn't mean the entire situation is fully resolved. That's not something that can be wrapped up so neatly. We have a lot more to uncover. How far this goes back, how long this has been going on, how it started, who it started with — all of those things. The FBI has a long and checkered history, and we'll be diving into that.

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We saw the Jeffersonian get hacked. How much scrutiny will that team be under as they try to free Booth?
: They will be under a lot of scrutiny. The one advantage they have is whoever is behind this knows that he or she has to now be very, very cautious. He or she doesn't know precisely how much information they have, how secure their system is, and if he or she plays their hand again and loses, they could be at risk for being uncovered. So, clearly at the end of this season it looks like a big loss for Booth and Brennan. On one hand they might have come through this in terrible shape, but in an odd way, they were victorious because Booth lived. He or she wanted Booth dead, shut down. Since that was not completely successful, that person is smart enough to know their own vulnerability. There's a chink in the armor.

Booth and Brennan's house was pretty much destroyed during that firefight. Should we expect a new set next season?
 If it were me, I would really not want to go back. That house has some bad memories at this point. It had some good memories, and then they were destroyed. That's another thing which reaffirms Brennan's commitment to shutting down whoever did this to them. 

What else can you tease about Season 10?
 I think we want to see an evolution in Season 10. Everyone has those times when they reevaluate their lives, or where they might want to take a different path or do what they've been doing in a different way. I think everybody has become very secure and comfortable in their situation, and life is not always that kind. So, I think there will be new challenges for Season 10 that have the potential to upset the apple cart. Everyone's life is changing.  Everybody is going to be evolving, It's a time in people's lives where they go, "Let me find out what it is I really want and how I can be most valuable. That's what we're drawing from for Season 10.

What did you think of the finale? Watch past episodes of Bones here.