The scene opens, and it looks like Madsen and Doc are asked to work overtime, and they are stuck in the office on a night of storms; and quite a storm it is. Doc goes to see what a worker is doing as he hears some noise outside, he looks in the hallway and soon witnesses a murder; much to his shock and horror. It is at the hands of the Ames Brothers, who have returned to the island due to some previously unfinished business and the team is thus faced with not one, but two returning prisoners, who seem every bit as dangerous as their previous inmates. In their day on the island, they were famous for nearly making an escape, quite a feat considering the fact that Alcatraz was considered to be a completely inescapable prison.
Back in the present, they manage to capture Doc, Doc is taken to the hole after the brothers find out he knows his way around the island; and thus he isn’t killed. Meanwhile, Madsen goes looking for Doc as she is by now worried by Doc’s long absence. She runs into one of the island's rangers. Or is he? Meanwhile, the brothers are able to lock Doc in a cell, who soon realizes that the two brothers weren't trying to escape at all, but rather looking for a rumored treasure; as usual he is so well versed in the history of Alcatraz that I doesn’t take him long to figure it out. The inmates are in fact looking for the legendary lost gold beneath Alcatraz, not only that but they have a third accomplice! A storm had knocked out the lights on Alcatraz (though not the security cameras), so most of what we see in the first hour was lit solely by flashlight. That constricted lighting, along with a rather gruesome slasher-style killing in the beginning, gave the episode an unsettling quality.
Soon, the third man is found it is a park ranger named Donovan; who Madsen had run into. He definitely does not seem to be down with the electric banana, had been working with the Ames boys back in the 1960s as part of a rather convoluted scheme. Apparently the three of them bought into the legend that the U.S. government had accidentally left behind gold on the Rock from Civil War days and they decide to do a little heist while they are doing some time (how they were planning on escaping with the gold was another matter entirely). Flash backs show that he was the accomplice. Their plan involved faking a religious awakening, lifting a key from Warden James and making a copy of it surreptitiously during kitchen duty; thus they would be on their way to carrying out their plan. Before it was over, one of them had his pinky sliced off by a meat saw and Donovan had to suffer a bloody beating that made him resemble Rocky Balboa for a second; thus their well orchestrated plan was foiled.
Rebecca Madsen does not initially know this; she is completely oblivious to Donovan being a criminal of any sort. Madsen starts to lead Donovan through the prison when she finds out that he is lying to her. By the time she finds out though, it is too late. The Ames Brothers have reemerged and start a shootout which leaves Herman Ames dead and Hauser injured. Hauser is shot through the side, but to quote the Black Knight, "It's only a flesh wound." Meanwhile, Doc calls his employee at the comic book store and finds out where the lock release is to the hole. Doc is able to escape from the cell that he was locked in, but as soon as he emerges, Donovan and Pinky Ames are there ready to kill; much to his dismay. They spare his life though; as they discover that he has an in-depth knowledge of the prison, they question him about the underground dungeon where the past inmates are housed, which is interesting. However, a flashback shows the brothers in the underground tunnels with keys that, they believe, will open doors to the gold.
The Warden informs them that they do not and confiscates the keys which look suspiciously like the keys that the prisoners who return to modern day return with; this after it is shown earlier that their plan which they had hatched with Donovan had horribly failed. The key in question is one of the hefty, mysterious keys we’ve been seeing since the pilot. When the warden caught the Ames Bros. back in the '60s -- before they had a chance to try it on the room they assumed held the gold -- he assured them that the key was to something else entirely. After failing to steal the booty in 1960, the Ames brothers suddenly found themselves alive and young in 2012 (along with their guard friend) and apparently decided the best thing to do was to stick to their 50-year-old game plan and get the gold; as they had failed miserably the last time round. Meanwhile, Madsen finds herself engaged in a final showdown in an attempt to save Doc. She takes off, enticing Pinky Ames to chase her.
She is able to get away and surprises Ames by dropping a metal frame bed on his head, killing him (while the other one she clobbers by launching a jail door at his head, which is gnarly and nasty). She finds Doc alive, but injured; they have spared his life, as they wanted information out of him. Now, they are only looking for the third accomplice, Donovan, who is still looking for the gold; he wants to finish the job he was unsuccessful at in the 60’s. Although the brothers have met their maker, Donovan actually manages to get into the secret room; thus managing what they hadn’t nearly fifty years ago. Although, in an attempt to open the door, he causes an explosion which leaves Hauser injured, but the door opens. Donovan is shocked that the room is empty; he can barely believe his eyes, and his shock and horror know no bounds. The gold is long gone from the look of things and he is captured by our heroes as he sinks into hysterical despair; his dream of fifty years shattered in seconds.
Instead of being a chamber of secrets, it is just a musty old claptrap, and in fact he surrenders to Madsen readily, without even putting up a fight. Although the two prisoners ended up dead, Hauser tries to get information out of Donovan; as he is the only link left. When Hauser interrogates Donovan later, we learn that Warden James might not be so dead after all; a truly interesting turn of events. "Has he come back? Is he the one willing to kill for these keys?" Hauser questions Donavon. At the end of the episode, although Hauser tells Donovan the gold was a fable, we are treated to a final flashback and learn that Warden James did indeed have gold hidden in the room in the past; depicted in images, with the warden actually standing with the gold bars. Hence they weren’t wrong after all. The episode ends.