“Bones” Season 12 will introduce a new serial killer -- one that will target Booth and Brennan -- in episode 4. Ray Mickshaw/Fox

[Warning: This articles contains major spoilers from the Season 12 premiere of “Bones.” Proceed with caution.]

Fox series “Bones” returned Tuesday with an episode that proved former squintern Zack Addy (Eric Millegan) isn’t the notorious serial killer known as The Puppeteer. It was actually his therapist at the psychiatric facility – Dr. Roshan – who framed him. Dr. Roshan was The Puppeteer.

This was one of the two most shocking revelations in “Bones” Season 12, episode 1. The other was discovering that Zack is actually the miracle doctor who has been helping Hodgins (T.J. Thyne) walk again. Unfortunately, Zack also revealed that Hodgins may not ever be able to walk again since the chance of that happening is only one percent.

Bones” co-showrunner Michael Peterson spoke to TVLine about the upcoming episodes. He told the website that Zack will return in episode 11. He also confirmed that Hodgins won’t walk again. “There were moments where we played around with [the idea of Hodgins] possibly walking again. But this just felt more genuine to people who do have handicaps. It’s okay [to be paralyzed]. Handicaps are real. You can still have a wonderful and fulfilling life. To do anything less would be disingenuous. So we resolve it by saying he’s going to stay this way and his life is going to be fantastic.”

Furthermore, a new serial killer will be introduced in episode 4. “This one is a little more action-oriented, more military-based. And this one is born out of revenge more than any other storyline,” Peterson revealed. Additionally, this killer will coordinate an attack at both Booth (David Boreanaz) and Brennan (Emily Deschanel).

While the team is solving cases and catching the new killer, Zack’s case will be reopened. However, they need to get evidence to prove his innocence and one way of doing that is by going over Dr. Sweets’ (John Francis Daley) notes. Booth will enlist Gordon Wyatt (Stephen Fry) to go over Sweets’ notes in order to set Zack free, reports TVGuide.

“Bones” Season 12 airs Tuesdays at 9 p.m. EST on Fox.