Bones postmortem: Jonathan Collier breaks down that huge finale twist

Warning: This story contains spoilers from the season 11 finale of Bones.

Bones is ending where it started.

Thursday’s season finale brought the team back into pursuit of a serial killer known as the Puppeteer — and all of the evidence is pointing to Zack Addy (Eric Millegan), a former Jeffersonian intern who, at the end of season 3, was sent to a psychiatric institution for helping a cannibalistic killer. In the final minutes of the hour, Zack returns to nab Brennan (Emily Deschanel), leaving the team on a race to find them both. But is there more to the story? As Bones heads into a shortened final season, EW caught up with co-showrunner and executive producer Jonathan Collier to talk about the decision to bring Zack back into the fold. (And be sure to check out Millegan’s thoughts on the twist here.)

ENTERTAINMENT WEEKLY: How did you decide that this would be Zack’s story?

JONATHAN COLLIER: It really came down to knowing that these are the last 12 episodes we’re doing this year. We thought: This whole next season is about wrapping up loose ends, finishing business that was started — relationships, characters, we want to tie up as much as possible. And we really want to make this a season that is exciting and meaningful, that pays off for our characters and rewards the fans that have put so much into the show. Once you come to that, who’s better to bring back than Zack? Because that was really unfinished business, and we’ve always been very, very fond of the character that [series creator] Hart [Hanson] created. I came to this show at the beginning of season 7, so for me it’s really gratifying to be able to make moves like this. And with Hart’s blessing. He’s been both helpful and supportive of everything we’ve been doing.

So you told him in advance that this was the route you were taking?

We would never take a move this big without talking to Hart. He would let us, but it’s just out of respect for him. He’s going to have a hand in the very ending of the show, and that’s very much by my and Michael [Peterson, co-showrunner]’s choice. Hart has been very open about the fact that once he handed the show over to us, it was handed over to us, but we really want him involved.

What were his thoughts on this twist?

He loved it! [Laughs] He loved it. He got very excited about it. I think his plan always was to wrap up loose ends. We had never talked about specifics, but I think he thought it was a great twist for us at the end of the season.

Did you all conceive of this serial killer arc with Zack in mind?

I think with any story that really works, and this is something that Hart taught us, you can have three or four likely candidates. And there’s going to be a lot of twists to the Zack storyline, by the way, so don’t take anything for granted. We didn’t think of this particular story with Zack in mind, but we thought of Zack. We thought of the character and of bringing him back eventually. And then this fell into place when we were breaking this story.

So how many episodes should we expect him for?

More than one.

Will we find out what’s been going on for Zack to this point?

Yes. We’re going to find out a lot. We don’t want to leave our fans guessing. We want to answer questions, and we want to reward them.

I noticed that Booth knew right where Zack’s room was. Does that mean that the team has been keeping in touch with him and paying him visits?

There’s a chance some have. There’s a chance some haven’t.

How is this going to affect the team? Can you say anything about how they’re all going to respond to this whole situation?

They’re going to question what happened in the past, and they’re going to have very different attitudes on how they should move forward.

Brennan in particular loves Zack so much. I can’t imagine that this is going to be easy for her.

Yeah, but don’t forget that Brennan is a scientist. She has to look at the evidence that she examined first. If she has any different approach to it, she has to ask big questions. She’s not one to change her mind very easily. We’re really going to get into the difference between Brennan and Booth here, and their approaches to evidence, and their approaches to having faith in people.

Was there any concern in the writers’ room about bringing Zack back like this?

No, people were on board. People wanted to see how we were going to service this storyline throughout the year, but that’s the fun of the writers’ room… Nothing’s easy, so you can’t say it writes itself by any means, but it gives us a lot of story, which is great, with a great character who deserves once again to be put through the wringer and to put everyone else through the wringer, too.

How do you anticipate the fans responding to this ending?

That will be very interesting. I think there will be a lot of excitement. I would hope. I mean, one of the great things about our fans is they don’t speak as one voice. [Laughs] So I think a good many of them will be very excited — as excited as we are.

Is there anything you want to say to fans who might be concerned?

It’s a thoughtful, meaningful move that we’re doing that really speaks to our relationships between all of our characters, and we’re taking it very seriously. It’s not something we would ever do lightly. We’re not playing with anyone.

On a happier note, Hodgins has some feeling in his legs again. Can you tease anything about what’s next for him?

There’s going to be a lot of positive movement in the next season, but not without a good amount of disappointment and struggle. Let’s just say his story resolves, but not in a way you might be expecting.

Can you tease anything else coming up about the final season?

Zack’s the first of the surprises. We’re doing a lot with our characters. We’re revisiting some stories that began very early in the series. It’s only 12 episodes, which is a blessing and a curse. It’s a curse because it’s fewer episodes. It’s a blessing because you can really make them tight and move them through an arc.

Is it mostly character storylines that are going to carry through, or the cases too?

Both. We have a new big bad for the year, who really speaks to the incredible DNA of the show — everything that Hart Hanson and Stephen Nathan did to build these characters and these stories. We’re really mining — they planted the seeds.

How about for Booth and Brennan? Anything in particular coming for them?

Yes! Really interesting, challenging, ultimately very rewarding things, but I don’t want to spoil too much. But the show is about them.

David Boreanaz directed this finale. How is it working with him as a director?

He’s a fantastic director. It’s unfair. [Laughs] You’re not allowed to be both a TV star and a terrific director, but he is. He pulled out all the stops. He has a creative vision, he’s got an amazing visual sense, he’s got an amazing sense of character. It moves beautifully, I think. It’s got such pace to it. He just did a fantastic job. He could have a long, great career as a director if he ever wanted to.