Fallout 4‘s Boston setting was confirmed in the announcement trailer after a few years of confident speculation among the fans. Post-apocalyptic Boston will incorporate many landmarks from what we’ve seen in the trailer from the Paul Revere Monument to the Bunker Hill Monument, to Fenway Park. We have not yet seen anything that the new game will include the Massachusetts Institute of Technology, known simply as ‘The Institute’ in the Fallout universe.
The Institute has become a secretive organisation since the fallout and has been referenced many times in previous games, thus leading to fans believing it should be a major plot point in the sequel. The Institute was referenced by Mr House in Fallout New Vegas when he revealed he studied there as a young man. In Fallout 3, a quest aboard Rivet City gives greater detail to the workings of The Institute.
In the quest ‘Replicated Man’ Dr Zimmer, under the employ of The Institute, is searching the Capital Wasteland for an android named Harkness. It is revealed The Institute’s advanced technology is able to make androids that are almost indistinguishable from humans, proven when you are asked to discover the identity of the android aboard Rivet City which in my opinion was a difficult task. The Institute used androids as slaves, though some would develop sentience and escape before being hunted down by the Synth Retention Bureau.
Any Fallout fan will remember the quest eventually concludes with you deciding the fate of the android Harkness and siding with the Synth Retention Bureau or The Railroad, an underground freedom fighter force aiding in the escape of androids from The Institute.
Another mention to this is the leaked Fallout 4 script making reference to the commonwealth minutemen that could be involved much in the same way The Railroad were in the Capital Wasteland.
Given the potential for story, characters and quests concerning The Institute, it wouldn’t surprise anyone to find out that it would make an appearance of some sort, on its home field of Boston.