The Fallout 4 Story Hints Hidden In Previous Fallout Games
Though Fallout 4 is the first game to be set in Boston, it's not the first Fallout game to mention it. Here are some hints at what might happen in Fallout 4's story.
With Fallout 4 moving its setting to a post-apocalyptic Boston, Massachusetts, it's expected that the game's plot will incorporate some of the city's most famous landmarks. In the trailers, we've seen footage of the USS Constitution, the Paul Revere Monument, the Bunker Hill Monument, and Fenway Park. But one landmark we haven't seen yet is the Massachusetts Institute of Technology, known simply in the Fallout universe as "The Institute".
The Institute has become a highly secretive organisation since the bombs fell, but it has been referenced a couple of times in prior Fallout games. By way of his obituary, it is revealed that Mr House, the primary antagonist of Fallout: New Vegas, once studied at The Institute. But the more significant reference comes in the form of a Fallout 3 quest called "The Replicated Man".
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The quest begins when you encounter a character named Dr. Zimmer. He is employed by The Institute, and is searching the Capitol Wasteland for an android, Harkness, that has escaped from his employers. Part of The Institute's secrecy concerns the highly advanced technology it houses; technology advanced enough to create androids like Harkness which are almost indistinguishable from humans. These androids are used as slaves by The Institute, but some of them develop sentience of their own, and subsequently desire to escape their life of servitude. If they do escape, the androids are hunted down by a group of law enforcement personnel known as the Synth Retention Bureau.
The whole quest is an homage to Blade Runner, in which "replicants"-- androids also virtually indistinguishable from humans--are hunted down and killed by a police force specifically trained to do so. As in Blade Runner, some of the members of The Institute's Synth Retention Bureau are androids themselves.
In opposition to The Institute and the Synth Retention Bureau is an underground movement calling itself The Railroad. This is a group of people who assist androids in escaping slavery and in finding a new life--sometimes going so far as to give them a complete facial reconstruction and erasing their memory to adjust to their new lives. In The Replicated Man quest, you must decide to side with either The Railroad or the Synth Retention Bureau by determining whether Harkness remains free, or turning him over to Dr. Zimmer.
It's highly likely that The Institute, The Railroad, and the conflict between androids and humans, will play a major part in Fallout 4's plot, given that we'll actually be exploring Boston. But how these factions' goals and objectives will play into those of the Brotherhood of Steel and Boston's other surviving groups remains to be seen.
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