The secret control room is often depicted as a secret in all of the Alcatraz episodes, until it is revealed in the end. The secret room is discovered by Hauser in "Garrett Stillman". He realizes that he has to the two keys to open the door, but is missing a third one, and all other alternatives to open the door fail.
He comes to realize that what the prisoners are after is the third key, and informs Soto and Madsen of this. Back in the past, the room is only shown once, as Warden Edwin James escorts Harlan SImmons down to it. He takes out the two keys (explaining their importance to the audience) and opens it, pushing Simmons in, telling him "Your future just got a heck of a lot brighter". The inside is not shown until the final episode.
Once Hauser and Lucy obtain the third key, they open the door which reveals a secret control room with old fashioned computers and a map of the United States with little red markers each with an Alcatraz inmate's number. It is then revealed that in the past, Tommy Madsen was used as an experiment for this. After having his blood returned to him with silver in it, the Warden gives Madsen the royal treatment. He takes him out of Alcatraz and tries to convince Madsen that he has no family left or anything good at all by hosting him at the restaurant where Madsen met his wife and then taking him to see his toddler son in Oklahoma, where Madsen comes to realize that he has no family after his son runs away from him.
Madsen returns to Alcatraz where the Warden takes him to the secret room, revealing the "Transfusion Man". He prints out a sheet of paper and begins reading what it says, the locations and the exact time that Madsen and the Warden were at. It was implied by Dr. Beareguard before that the silver in the inmate's blood could be used as a tracking device. The transfusion man tells Madsen that he will be their first man in whatever experiment they're planning. The scene is then cut from there to the future, where Hauser looks at the map of the States. The red markers reveal that the prisoners are located not just in San Francisco but the entire country. He and Lucy hear a noise and they go into another part of the room where they see the Transfusion man not having aged, passed out, barely awaking (presuming that he might have just jumped from the past). The floor is a mess with old food wrappers and his broken glasses at his side. He wakes up, asking "Madsen?" but Hauser responds introducing himself. The Transfusion man then asks what year it is, to which Hauser responds 2012. The Transfusion man ends up laughing like a madman (showing that he is the one responsible for the jump) and the scene cuts, and the real purpose of the room, rather than to track the inmates, is never revealed.