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For years, fans have been begging for the return of a fan-favorite character from “Bones” early years, and the Season 11 finale finally gave it to them — in the worst way possible.

The team’s search for the brilliant yet terrifying Puppeteer culminated in the shocking revelation that the murderer they’ve been hunting is actually none other than Zack Addy (Eric Millegan). At least … he probably is.

Die-hard fans will remember Zack as Brennan’s (Emily Deschanel) kid-genius assistant from the first three seasons of “Bones,” who flamed out (quite literally) thanks to the manipulations of another serial murderer.

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Now, he’s back, and it seems like Brennan’s subconscious has been trying to tell her who the killer is all along.

The horrific nightmares of burned corpses and shadowy figures that plague Brennan at first seem to be leading to her new therapist. However, after further study, she remembers that Zack is the one who suffered serious burns to his hands during his days under the Gormogon’s tutelage.

Unfortunately, it seems she made the connection a little too late, and Zack kidnaps her before she can get herself to safety.

How he manages to kidnap her is another question entirely, since he’s supposedly been locked up in a psychiatric hospital the past eight years.

Is he really brilliant enough to have killed all these people without any of his nurses or orderlies realizing he’s been taking murder field trips? Or is this all some demented plan to protect Brennan instead? That last terrifying shot has us excited, nervous and most of all confused!

To help us figure it all out, executive producer John Collier spoke with Zap2it about “Bones” plans to finally reintroduce Zack Addy into the mix.

“We knew we wanted to bring back Zack at some point,” Collier says. “I think it really became a step we definitely were going to take when we found out [Season 12] would be the last season of the show. So we wanted to do it before the show terminated.”

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In the past, “Bones” creator Hart Hanson addressed the possibility of Zack’s return, but he voiced doubts that the audience would even recognize the character after he’s spent such a long time away. “We have a pickle with Zack,” Hanson remarked the 2012 Paleyfest panel, “There’s a group of people who’d like to see him again, and then there’s a larger group who don’t remember him.”

We remember Zack though, and Collier says they don’t expect the audience’s past memories of the character to be too big an issue. “He’s such a strong character, he’s such a good actor, you can do so much with him that you wouldn’t have had to see the early episodes to find this very satisfying.”

We also had the chance to chat with Eric Millegan about his return to “Bones,” and what his homecoming was like now that he’s finally returned to the show.

“They asked my agent if I was available for two episodes at the end of the season, and my agent emailed me, and I said, ‘Holy crap!'” Millegan jokes. “That’s what I emailed back. I said, ‘Yes, I’m available! Yes, I’m interested!’ It’s thrilling because that doesn’t happen to everybody’s career. I’ve been off the show for years, but to have the opportunity to have this happen to my character and to have this happen to me as an actor is thrilling.”

RELATED: ‘Bones’ EP promises Season 12 will be ‘what the fans want’

As far as where we’ll find Zack when Season 12 picks up, Millegan says we should be prepared for a very different character than we remember from “Bones” early seasons — in all the best ways, of course.

“He’s been in a mental hospital for eight years. He’s been through a lot, and we’re going to find out what he’s been through.” Millegan says.

We’ll have to wait until 2017 when “Bones” returns for its twelfth and final season to find out exactly what Zack has been through and what sort of changes that will bring out in him. Millegan did tease that they’ll begin filming Season 12 very soon though, and he’s excited for fans to see what the writers have cooked up for Zack.

“I’ve read episode 1 [of Season 12] and it’s amazing,” Millegan says. “It’s really, really good. It’s very fun, and it’s a lot of Zack. Fans will not be disappointed when they find out what Zack has been up to for the last eight years.”

“Bones” is set to return in the spring of 2017.