Bones Fall Finale: Executive Producer Michael Peterson Clarifies That Heartbreaking Cliffhanger

Marisa Roffman
Bones Spoiler Alert
Patrick McElhenney/FOX

Spoiler alert! Do not read this post unless you've seen the two-part Bones fall finale!

Bones dealt a powerful blow to the show's "King of the Lab."

The second hour of the two-part fall finale, started off brutal enough: Cam (Tamara Taylor), Hodgins (TJ Thyne) and Aubrey (John Boyd) were investigating remains when a bomb—hidden in the body—exploded. Cam, who was nearby on a call, was safe, but Aubrey and Hodgins sustained injuries; Aubrey's were more severe, as he pushed Hodgins from the scene and then sheltered him from the explosion. Hodgins was able to walk out of the hospital, whereas Aubrey underwent surgery to treat his wounds. But appearances were misleading, and after the case was solved—and just after Hodgins and Angela (Michaela Conlin) decided to try for another child—he collapsed. A trip to the hospital revealed that Hodgins was paralyzed, and the damage he sustained in the explosion had set in 24 hours after the initial injury.

Surprisingly, Hodgins's injury won't be a decision Bones undoes in the next episode. So we spoke with Bones co-showrunner Michael Peterson about Hodgins' new way of life and how it will impact the team, plus the time jump and the new serial killer that fans should expect when the show returns in 2016.

RELATED: Still Reeling From the Finale? TJ Thyne Speaks About That Huge Twist

Why did you decide to paralyze Hodgins? And what conversations did you have about it with TJ and the rest of the cast?
It was something we played around with doing for the season opener, but some other curveballs were thrown our way, so we went a different route. [But] our first phone call, after we came up with this idea, was to TJ. His [response] was, “Yes, yes, yes. A thousand times, yes.” Once he was excited [we were set]; TJ’s instincts are amazing. We had the Betty White episode earlier this year, and a big part of why that worked was because of him. He was like, “I want to be tranquilized in it.” He played it magnificently; his instincts are good, and I always trust him. When he got so excited, we knew we had something great here.

Part of the reason we did it is because, when Jon [Collier] and I took over as showrunners this year, David Boreanaz said, “Go back and watch the early seasons; try and recapture some of that early magic.” And we wanted to do that with a little more banter back-and-forth between Brennan and Booth. Make sure they were not just a loving couple who never get dark. Also, we went back to some of the earlier stuff and looked at Hodgins, and there was some good stuff where he was a bit more angry. So, needless to say, angry Hodgins will be revisiting us, as he is now in this wheelchair. TJ is such a fantastic actor. To give him this challenge... it’s obviously going to affect everyone in the lab, but primarily Hodgins and Angela. He really is going to go through every possible emotion as he deals with this injury.

On a practical level, the lab doesn’t appear to be very wheelchair-friendly. How much will that be addressed, and how will Hodgins be navigating that?
Right now we’re filming episode 12, and we have a really beautiful scene where [Hodgins], for the first time, is seeing the lab not as his usual self, but as someone with limitations. You have this platform, where they do half of their work, and there are stairs [to reach it]…there will be a lift provided for him, but his life, as he’s known it, is over. Our show has these challenges because of the limitations of the lab, and that just helps us feel more confident we’re making the right decision.

Since this was something you originally planned for the premiere, is there anything you had planned to tackle that you won't now? Was there anything you were able to refine or revise as you planned things out?
I think we’re going to get everything done that we wanted to. I’m not worried about the limitations. Thankfully, it’s not cable, we get 22 episodes; we get lots of time to play with this. Jon and I have always said publicly, our plan is to keep going for as many season as possible. And TJ is the most committed actor I’ve ever seen when it comes to this. When he’s on the lot, he doesn’t leave his wheelchair. He came in for a meeting the other day, and he rolled all the way from Stage 9 to [the Bones office]. [He's] had some [cords] wrapped around his legs so he could lose feeling and know what that was like. Everything you’re going to see him do, as far as physical therapy and getting out of the chair [for that], he really is going to be dead lifting. He’s just absolutely amazing.

Were there any earlier versions of this story where the entire team was there, but only these two got hurt? Or did you always feel they needed to be separated when the bomb went off?
When it was originally written as the season opener, Booth and Brennan were gone—they were still taking their time off. So, it was always kind of conceived with Booth and Brennan not being on the scene.

How will Hodgins's injury impact the show’s tone?
We hope we’re not going to make it a constant darkness. It’s one of those things where there are several different stages [of grief] when dealing with something like this. You have the denial, the depression, the anger, and all these other emotions. But, eventually, you do want to get to a place where there is some degree of acceptance. So, this is a bad injury, but at the end of the day, we’re also very humble about it. There are a lot of people who have to deal with injuries like this. They find their moments and they go on and have great lives. Being handicapped is far from being the end of the world. There will certainly be moments when it’s hard for him to accept, but then there will be others when he can even find blessings in tragedy. Our goal is not to tell an entirely different show. We want Hodgins to go through this process, but it won’t affect Bones as we know it. It will still have its lightness. And TJ will provide a lot of the humor. I think we’ll have times where he feels more like Dr. House than Dr. Hodgins. But we will see our Hodgins again.

Should fans expect that Hodgins will remain in the wheelchair for the duration of the series?
For right now, yeah. You look at it, and there are series that have done it well, and series that haven’t. The Downton Abbey thing didn’t sit well with me; Matthew was standing very soon after. So I think we’re trying to differentiate ourselves. But for right now, TJ is doing well with it, and we have a lot of stories to tell. Certainly, as far as we’re concerned right now, he’s paralyzed and he’s in the chair.

Bones - Season 11 fall finale

Jennifer Clasen/FOX

(L to R) Michaela Conlin, Tamara Taylor and TJ Thyne

How is this going to impact Hodgins and Angela and their relationship?
It’s going to be very hard. For Hodgins, as someone who pursued Angela, he always felt very blessed to be with her. I think this is going to change his outlook a little bit. I think he’ll have self-doubt about whether or not he’s worthy. He’s going to be angry, he’s going to be depressed, he’s going to be going through every emotion possible. She, being the one closest to him, is going to be the one to bear the brunt of a lot of his emotions. It’s definitely going to strain their relationship. There will be, for lack of a better word, temptations on all sides; maybe find an easier way out. It’s going to test them as nothing has on the show.

Other people as temptations, or something else?
I think there will be both.

Will there be a time jump between tonight’s fall finale and when the next episode picks up?
Yeah, it’s going to be about two months. We’re going to get him through a decent amount of physical therapy, and it’s going to be a bit of a jump.

How will the Jeffersonian team have been handling the news in the time jump?
I think they’re shaken that it’s happened, but they’ve had time to adjust. There’s the injury itself, and then there's how he has changed in the meanwhile. I think that’s the biggest adjustment: not the physical nature of it, but the emotional. That’s what they’re going to have to deal with the most.

Brennan has had a lot of vocal concerns about Booth’s well-being in the past few episodes. How much of that is acknowledging where they have been in the past year, and how much of it is foreshadowing?
I think it’s both. It’s definitely both. It’s been a dangerous last couple of years for Booth. He has a tendency and a way to put himself in harm’s way. So, it’s definitely a past, but it’s also definitely foreshadowing what’s to come.

Booth and Brennan also took time away from their jobs between seasons. Will they—or anyone else on the team—reconsider their job in the wake of Hodgins’s injury?
That’s not the focus, but there are repercussions of all this going on. We will explore the decision to quit in the first place. Some unforeseen elements—some guilt—will rear its ugly head, starting with episode 13 with the introduction of a new killer.

Is this related to one of the cases that didn’t get closed when Booth and Brennan were away?
I will not say. But you are an astute watcher.

Bones - season 11 fall finale

Patrick McElhenney/FOX

(L to R) Guest star Pej Vahdat as Arastoo, Emily Deschanel, Tamara Taylor and Michaela Conlin

When we last saw Cam, Arastoo had just told her he wanted to fight for their relationship. Where will we find them after the two months?
In the first two episodes back, Arastoo is not there. They more or less put themselves on pause. He’ll be back in episode 13, and it’s very difficult for [Cam]. She’s trying to balance where she is with him, where she is with Sebastian. And [Arastoo] is trying to figure out what matters in his career. I think it’s tough for Cam. She put herself out there, and in a way, they’re back to where they were: she’s still nervous that one of the two of them will resent the other. They’re in a tough place where they know they love each other deeply, but it’s [sometimes] an impossible relationship that just can’t work out.

While she’s on pause with Arastoo, is Sebastian aware of what’s fully going on?
Yes. He’ll know what’s going on, and it’s tough for him. He fell for her very quickly, and thought there was more potential than there is. But there’s always danger of being the relationship after a really important one. He’s practical in a way, and Sebastian will play in heavily for the rest of the year.

With Angela as well?
He has a relationship with her; he’s her mentor. But it’s a different capacity [compared to] his relationship with Cam.

How is Aubrey dealing with Hodgins’s injury, given they were in the explosion together?
Aubrey is at least practical enough that he knows he did everything he could. Yes, Hodgins is paralyzed, but he would be dead, otherwise. Aubrey is a professional as far as that goes…we’re going to have some other elements we’ll be playing with him for the rest of the season. I think it bothers him…but he’s not going to wallow in guilt; it’s better to save someone’s life.

Looking ahead to what you have in store for the second half of the season, what can you preview?
Episode 13 introduces the new serial killer, who we’re very excited about. Probably the creepiest case we’ve ever done. I keep getting looks from people; it’s one I wrote myself. People are wondering: Do I have another side to me that is really dark and twisted? What’s wrong with me, why would I come up with this? There’s something about the last name Peterson—we kill a lot of people: [real-life killers] Drew Peterson, Scott Peterson. Michael Peterson. But I’m going to choose to take that as a compliment, somehow. It is a bit of a darker territory than we’ve gone before. It’s something I’ve always wanted to explore. It’s a very, very creepy episode, and it will not be solved in the first case… it will lead to probably one of the bigger twists we’ve ever had on Bones. So when episode 13 comes along, don’t watch it by yourself; have someone to hold on to.

Ian Toynton came back to direct an episode of Bones. Is there any word on whether former Bones showrunner Stephen Nathan will pop by to write another episode?
We would love it if he would; he’s family. I hope he would. But we don’t have it on the board yet.

Any other cases of the week coming up that you can tease?
One we’re breaking right now that I’m enjoying a lot is, we have [the death of] a Secret Service agent, and this is someone who is assigned to the president, and someone who has gone on a scout to make sure the area is safe. We find that person dead, and the question is: was he killed for personal reasons, or was it an attack on the president? And Booth is going to be, pardon the pun, in the line of fire on that one: he’ll be joining the Secret Service on special assignment. That is one I can’t wait for. One that will be amusing and on the lighter side is, we’ll have an a cappella episode. It’s [from] our script assistant; she’s going to be writing it; she’s been a star, so we want to reward that. It’s going to be a very fun episode, and we’ll learn a bit about Aubrey’s past in the a cappella episode. Take that as you will.

Are there any guest stars coming up?
Nothing planned right now. Most of the time, we just write the episode, and if someone fits in perfectly, then we try to cast them. But we are excited that Sara Rue, who was in episode 10, will be coming back to do more episodes. She was fantastic. We’re excited to have her back. And, who knows, Betty White always tells us she wants to come back, so we may have to have Dr. Mayer back.

With the show’s future uncertain, how are you approaching the end of the season?
There’s a million conversations to be had. Jon and I have a cliffhanger to beat all cliffhangers in our minds, so that’s our goal: to aim towards that. But if someone gives us a phone call and tells us to do otherwise, we will. But that’s certainly our inclination.

Bones returns in 2016.