Sam Neill and Sarah Jones

Only a month in to its freshman season and Alcatraz has already raised many mysteries. We've been dissecting them each week in hopes of figuring out the answers.

To recap: San Francisco detective Rebecca Madsen (Sarah Jones) and Alcatraz expert Diego Soto (Jorge Garcia) were enlisted by federal agent Emerson Hauser (Sam Neill) to track down a group of Alcatraz prisoners and guards who mysteriously vanished into thin air in 1963. Dubbed the '63s, the men are returning to present day with missions to track down keys that apparently unlock a secret "downstairs" door at the prison where... well, we don't know that yet, but we do know the prison doctors were taking the prisoners' blood, and Tommy Madsen (David Hoflin) was begrudgingly at the center of it. 

Dissecting Alcatraz's Mysteries: Who are the '63s?

TVGuide.com turned to executive producers Jennifer Johnson and Dan Pyne to answer some of the questions we've been keeping track of. For instance: Who are the powers that be that are behind the '63s' disappearance? We may be meeting one of them soon! 

Will the reason why Tommy Madsen is so important come to light soon?
Dan Pyne:
Yes. Everything's building towards that in midseason. That would be the question that's answered in the last episode.
Jennifer Johnson: A lot of things are going to come together having to do with the inmate's blood, Tommy Madsen and what's behind the Warden's door.

Is there a particular reason why Alcatraz prison became the focus point of the disappearance?
Johnson:
Yeah. There are theories that our characters have. We'll talk about what those theories are by the end of the season, but they may not be the real ones. We'll understand what Hauser thinks about it and what his think-tank thinks about it, but that's really just the tip of the iceberg. We may meet a character by the end of the season who does know that specific answer, who probably has a lot more answers than any of the characters we've met so far.

Dissecting Alcatraz's Mysteries: How many '63s are working with Hauser?

Will we learn who the powers that be are and what their motives are this season? Or is that a series arc?
Pyne:
Well, it's a little of both. I think by the end of [Episode] 13 we'll have an understanding of who that might be.
Johnson:
That's the character that we were referring to. He might be part of the powers that be.
Pyne: But definitely by the end of the season there will be more of a sense of the game that's afoot. We won't be coy about it and keep holding back. There will be a better sense of what's going on. We may not understand what the endgame is, but at least the players will become a little bit clearer.
Johnson:
It's complicated because they don't all have the same goals, which we're going to hit upon before the end of the season. There's almost a secret war happening between the '63s, too. That all interplays with what their relationships were in the past when they were imprisoned or working on Alcatraz.

Is there a reason why some of the '63s have gone against mission?
Pyne:
Yes.
Johnson: We won't say definitively, but we'll give people the tools to have pretty informed theories about it.

What's with the fascination with the number three — three keys, three bank robberies and three days of sniper shootings are just some of the few?
Pyne:
There may be more than one number clue.
Johnson:
Forty-seven is an important number, too. But we like three for its stability and the idea that it's a triangle. We talk about triangles a lot and relationships that have three angles in them.

Dissecting Alcatraz's Mysteries: Who is Lucy, really?

Lucy had mentioned in the past that she was going to fix the prisoners with memory-altering experiments. Did she end up being a puzzle piece in the overall mystery of how the '63s disappeared?
Pyne:
She definitely is a puzzle piece, yes. We may not stick with this forever, but right now, everything that's happened in the past has happened chronologically in 1960. So, there's still three years left before the jump. Clearly, allegiances change. Stuff happens in those three years between the time when Lucy comes to prison to start her experiments and 1963 when she obviously disappeared along with everybody else. Certainly, she has some answers to what might have gone on, but she also may not even understand. She didn't understand at the time what was going on. It may be just now looking back at it that she can start to unravel what she saw.
Johnson:
Yeah, helping the team unravel by knowing the psychology of the inmates. But the Warden (Jonny Coyne) is very Machiavellian. He does not want the left hand to know what the right hand is doing. So, he may utilize different players for their different challenges. But part of his M.O. is not to let any one person know too much of what is going on.

Diego mentioned in the pilot that the Warden had died many years ago. Did he really or is he part of the missing '63s?
Pyne:
It's possible.

Will we discover how Lucy came to work with Hauser in the future and see more of their relationship in the past?
Johnson:
Yes. Definitely, 100 percent.
Pyne:
Their love story is one of the great triangles of Alcatraz.
Johnson:
It's kind of the love triangle between Hauser, Lucy, and the jump itself.

Dissecting Alcatraz's Mysteries: Why is Tommy Madsen so important?

Will we find out what Dr. Beauregard (Leon Rippy) was doing behind closed doors at Alcatraz?
Pyne:
You may find out soon, in the next couple episodes. Then once you find out, you may be totally wrong, but you will see some of what he's up to. He's a little bit jealous of Lucy's elevation to the prize poodle on Alcatraz, so he gets up to some hijinks that he maybe shouldn't.

What can you tell us about the downstairs door that needs to be opened with three keys?
Johnson:
That we're going to open it before the end of the season. We'll understand by the end of the season what's behind that door, at least one layer of it. It was very important to the Warden. There may only be one person that he shares that secret with.

We learned Diego was kidnapped at age 11. Will that come back into play?
Johnson:
That's his deep, deep back story and a lot of what motivated his fascination with Alcatraz and with comic books. We won't necessarily go there before the end of the season, but that is part of who he is as a character and why he became part of this team.

Dissecting Alcatraz's Mysteries: Hauser and Lucy's past revealed

Once Rebecca does finally come face-to-face with Tommy, will she be able to let bygones be bygones and realize that he is still her family?
Pyne:
Gosh.
Johnson:
We know the answer to that, but I don't think we can tell you.

What can you tell us about what is in store for her?
Pyne:
She begins to get a little bit more focused on solving the mystery of what happened to her partner and delving into that day and why he was there. It slowly leads her to some revelations about her partner about the larger mystery of Alcatraz and also about Tommy Madsen.
Johnson:
And what everybody is doing here present day. They discover that there are different factions of '63s here in present day San Francisco and beyond.

Alcatraz airs Mondays at 9/8c on Fox.