Alcatraz, Jorge Garcia and Sarah Jones Alcatraz, Jorge Garcia and Sarah Jones

Hopefully Fox picks up Alcatraz for a second season because the two-hour season finale left viewers with plenty of new questions — and one possible major death.

In the season ender, Rebecca (Sarah Jones) finally came face-to-face with her grandfather, Tommy (David Hoflin), who is apparently one of the lieutenants on the side of the '63s faction who work for the Warden (Jonny Coyne). The other side is lead by Harlan (Steven Grayhm), and possibly Matt Craven's mysterious man (whom we'll call MM throughout the story since he has no name) behind the door. What are their ultimate goals? Still not completely clear, but we do have a new theory. Why were they divided? Somebody broke a promise. Let's first take a look at the season-long mysteries that were answered, then dive into the new questions that the finale raised:

Alcatraz Scoop: Tommy vs. Rebecca and 6 more spoilers from the season finale


 Who's behind the mass disappearance?
The Warden and the MM, who turns out to be quite nifty with science. (We're guessing there are still others besides these two whom we have not yet met.)

Did the Warden know the mass disappearance was coming?
Yes, because the MM told Tommy in 1960 that within three years (a.k.a. 1963) he would be back out in the world.

What caused the jump?
The brain trust thinks it was caused by a geo-thermal event, possibly a tectonic plate slippage. If that's true, it explains why San Francisco, the earthquake capital, was ground zero.

What was the jump like?

Still unclear, but Lucy (Parminder Nagra) did note that it's not about missing old record players, it's about missing the people with whom you listened to the records.

What's behind the door downstairs?
A map of the United States that tracks the returning '63s and their projected return locations based on the silver in their blood.

Why hadn't Hauser (Sam Neill) discovered the door downstairs in present day?

A wall was built over it.

Why is Tommy important?

He was handpicked by the Warden and the MM to be patient zero (in a sense) after the MM observed him in Korea. He was going to be their "advance man," meaning he'd be the first sent through into the field.

Why were they taking Tommy's blood?
Still unclear, but possibly to free up room for the silver to eventually be added back in.

Why are the '63s fighting against one another?
Because of the keys that unlock the door downstairs. Tommy Madsen works for the Warden, while Harlan is either acting alone or under the guidance of the MM.

Why was Rebecca (Sarah Jones) chosen to work on the taskforce?

Besides the obvious that her grandfather is one of the '63s, Rebecca was chosen because she doesn't shoot first and ask questions later. She was also championed by Lucy, apparently. 

Why did Tommy kill Rebecca's partner?

Her partner was paid by Harlan to keep tabs on Rebecca in order to get to Tommy and the rest of the '63s.

Why didn't Diego (Jorge Garcia) know Lucille had worked on the island?

The Warden kept it secret from the public.

Why was Lucy working at Alcatraz and doing experiments?

Simply to get to the root of the criminals' deviant behavior in hopes of fixing them.

Why was Hauser so freaked out upon discovering every inmate missing?

It wasn't for the obvious reasons. It was because Lucy had also disappeared.

Why aren't Lucy and Hauser back together now?
He's not the same man that she fell in love with 50 years ago. A part of him is missing, Lucy said.

Why did Cobb (Joe Egender) shoot Lucy?

She was his only target, not the taskforce, and as long as she's alive, she'll always be a target. (Why she's a target remains to be seen.)

Why did Ray Archer (Robert Forster) leave Alcatraz?

Tommy essentially forced him to leave the island, which was part of his deal of working with the Warden. 

Why do Lucy and Beauregard (Leon Rippy) like each other now?

Likely because, as fellow '63s, they went through this together.

Alcatraz Exclusive: Crimson Tide's Matt Craven to play one of the powers that be


Is the Warden back in the present?
Seems unlikely since Hauser's military advisor asked if Tommy's reappearance signaled the return of the Warden. (Plus, the producers mentioned that the '63s aren't returning at the same time.) The MM, however, seems to have returned during the finale, so we hope the Warden is not too far behind.

Which of the side effects is Beauregard worried about?
After giving Lucy Porter's blood, he was wary to let her out of the lab and mentioned that there could be side effects. Could this mean that she may run the risk of jumping again? She could end up being a serial killer and take on Porter's traits? What we do know for certain is the silver in the blood will now never be out of her system.

What caused the rift between the Warden and E.B. Tiller (Jason Butler Harner)?
Their animosity for each other and power struggle has been building over the last few episodes, but it remains unclear what set it off.

How did Lucy know about the door downstairs?
The Warden seemed to keep everything secret, so how was she aware of it and able to tell Hauser about it? (Hauser also seemed to inadvertently know, calling it "The Warden's door" upon seeing it, and knowing exactly what keys to use.)

Who is really in charge of the '63s?
It seemed like the powers that be were providing the '63s with everything they need to assimilate to the future, but Tommy was revealed to be Stillman's handler. Tommy is working for the Warden, but not every '63 is working on their side. Others, like Ghost — a prisoner who the Warden claimed had died after an escape attempt — were working for Harlan.

How did Harlan become so powerful?
The Warden rigged the parole system to get Harlan off the island. He set him up with a friend (the MM, perhaps?) to take care of him so they could eventually be in touch. But how did Harlan become a billionaire? And why hasn't anyone seen him in decades? And why isn't anyone allowed to see him? Maybe he isn't aging? It was also noted that Harlan broke a promise to the Warden, which put them in opposition. What promise was that?  Is Harlan working for MM?

What are the '63s trying to gain by carrying out missions?
Most of them have been trying to track down the keys to the door downstairs. Does that mean they want the power to track down the other '63s or is there something more sinister going on down there?

Dissecting Alcatraz's Mysteries: Lucy finally wakes up!

Why are the prisoners returning all over the country?
According to the map, there are other '63s spread out across the country. How did that happen?

How did the silver in Tommy's blood help him to jump?
Not every '63 has had silver in their blood, otherwise Lucy would've been treated sooner. So why was the silver so important to the overall plan?

Is the President of the United States in on the '63 cover-up?
He was briefly mentioned in passing, that even the President couldn't get an audience with Harlan. Does the conspiracy go that high up?

What happened to Hauser in Paraguay?
Since Lucy will always be a target, he planned on taking her there to keep her safe, but not staying himself because of a previous incident there. What happened? (We may never know since Lucy decided to stay in San Francisco to see the mission of capturing the '63s through.)

How did Rebecca's parents die?
Apparently Rebecca didn't know what really happened to them because she looked confused when Tommy asked if Ray told her how they actually died.

If he was protecting Rebecca, why did Tommy stab her in the stomach?
Tommy noted that he was protecting Rebecca by killing her partner, but then he turned around and stabbed her in the stomach. Why, Tommy, why? Rebecca flat-lined in the closing moments of the finale, with the doctors calling time of death. However, if Tommy can withstand an infusion of silver, why can't Rebecca be brought back to life the same way? Please?

What did you think of the Season 1 finale? Should Alcatraz be renewed? In case you missed our previous Dissections:
Week 1: Who are the '63s?
Week 2: How many '63s are working with Hauser?
Week 3: Who is Lucy, really?
Week 4: Why is Tommy Madsen so important?
Week 5: Hauser and Lucy's past revealed
Week 6: Will the '63s ever age?
Week: 7: Is the Warden a '63? Or is he pulling the strings?
Week 8: Why were the '63s being brainwashed?
Week 9: Lucy finally wakes up!