In the 50's, an alien spacecraft crashed. There was one alien survivor that was initially taken to Area 51 for study. Due to the government pressure and increased public awareness of Area 51, the government was forced to move the alien to a different location, Alcatraz. Who would suspect that an alien was being held at Alcatraz in a "state of the art" underground lab.
One thing that was learned from the alien study was that it's blood had special qualities. Mixed with human blood, it had the ability to clone humans and maintain a large portion of their memories, attitudes, etc. A side effect was that they did not age. The objective was to reabilitate inmates by removing whatever defects they had, specifically the ones that got them put in jail and then release them back into society for live monitoring and testing. That became unimportant once they discover the anti-aging qualities (big mistake). As part of the bargain, the alien was promised release once the experiment was complete. I'm assuming that they were able to communicate with it. The Doc and Lucy were cloned, but were against the testing once it became only focused on the anti-aging effect.
The process of cloning was very painful and initial tests failed miserably. Several inmates died as a result. Once the process was deemed a success, word got around about the "fountain of youth" and several guards and staff wanted in on the prospect of living forever. In 1963, when Alcatraz was scheduled to be shut down, a collective group of cloned inmates, staff, and guards decided to leave the island and go into hiding. Some of the staff were never cloned and were left behind. The government couldn't admit to losing everyone, so the whole thing was swept under the rug.
What about the alien? It was left behind and locked in the secret labratory, never to be seen again. Now the kicker....everything was fine until aliens came back to search for their lost comrade. What seemed like several years to us, is actually a very short period of time for the aliens, so little time has passed in their world. Another unique thing about this species of alien is that it has the ability to communicate telepathically. Since it's blood was used in the cloning, that ability was passed to the human clones. The captured alien has no idea where it is being held, but the clones do. The alien rescuers start using the clones to find their comrade. The clones know the island well and where certain thing went after it was closed. They know where to find thing like the keys used to unlock the labratory which were taken from the island by the staff that was never cloned.
Two things are at risk here. The government never wants to admit they have an alien in captivity and they don't want to admit that they somehow misplaced 300+ prisoners. In comes Hauser. He knows that Lucy and the Doc were part of the experiment but they never went into hiding. With the help of Hauser, they have been trying to find the inmates for 49 years, building up their research facility on Alcatraz. Their mission is to catch the returned inmates before they kill more people and expose the government. However, they must let them get to a certain point in their quest so they can recover clues, such as the keys. Remember that the clones are exactly like the originals, they are killer.
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