Let me, a real Bostonian, solve all the hoopla over the retarded Institute-centric plot bubble, by proposing my own. (This may or may not cause more anger, and this post is meant to be satirical)
How about that you are chosen from the myriad groups of Massachussets raiders as a new member of the Institute (which makes a <4 intel. character rather humorous in this plot), in what is totally not a dark parody of college applications, and you turn out to be a lab rat in an experiment that could potentially save humanity, but would kill you.
Being the scumbag Raider you are, you run like a little bitch from your chance to become a McGuffin, and trash the place. Now, you have to fight your way through a postnuclear Boston (complete with clam chowder and armies of people who sound like Peter Griffin), while hounded by the seemingly infinite technological horrors of the Institute.
At the end of the story (or eating everything that's left in Faneuil Hall), you get to blow the fuck out of the Institute for harrassing you, and as a back-handed thanks for giving you the chance to become the most badass living thing in Boston.
OR...
You go through with the experiment, and miraculously live
You are now a McGuffin.
As such, the Institute decides to have you excise your powers and conquer the various Bostonian tribes and introduce them to the wonders of modern medicine, toilet paper, and clam chowder made with actual (cloned) clams.
At the end of this storyline, your McGuffin powers go nightmarishly wrong and you ascend to a higher dimension of existence in a ball of fire, thus destroying Boston.