TLDR: the Institute accidentally created their own master-like entity that screwed with a lot of Institute data.
So, I was watching a lets play of fallout 1 (love the story, can't stand the gameplay) and I had a thought that might drastically improve, or at least help explain, the Institute storyline and wondered what you guys would think.
A big question with the Institute is why were they messing with super mutants for so long with no good results? Well, sometime long before the game began, the Bioscience division created a master-like entity during their super mutant experiments and the master basically either consumed the director of the bioscience division (and every subsequent director) or convinced them to join him and effectively ran the division itself. Like the original master, it also absorbed computers which it would use to falsify information about the successes of the super mutant experiments while also sabotaging the other divisions of the Institute.
Like the original master, its answer for the wasteland was to convert everyone into super mutants. This master, however, realized that super mutants couldn't breed and had to spend a long time trying to fix the issue (and ultimately never succeeded).
Think about it, why did the Institute give up on cyborgs like Kellogg? The master manipulated information to make it appear that all cyborgs like Kellogg would become psychotic. Why didn't the Institute consider gen 3 synths real? The master manipulated information to ensure that it would seem that gen 3s can never be like them. Why didn't they expand their plant growing operations onto the surface (until Warwick homestead at least, which is relatively new)? The master forged data proving it still wouldn't work on the surface. Who really caused the CPG massacre? The master sent the synth that caused the massacre, seeing as how if it had succeeded, the Institute may not have wanted to continue making super mutants that pretty much solely fucked with the surface.
Long after the master was created, Brian Virgil comes along and eventually figures out what's going on and tries to tell Father about it. Father doesn't believe him and Virgil does his thing, turns himself into a super mutant, a version the master is not using and that Virgil has the cure for, and breaks out.
Father then goes in to check out whats going on and finds out the Virgil was, in fact, right. Father kills the master and discovers that for years (probably before Shaun was ever even brought to the Institute) the master has been manipulating the Institute's data so that super mutant research could continue and would appear to be the most successful division. This leaves Shaun completely hopeless. Almost all data collected for so long is potentially blatantly false or at least fully questionable.
This feeling of hopelessness is what convinces Shaun to release his surviving parent. He is at a total loss. It also gives, an admittedly still not great, reason that he ends up putting you in charge. All of this data they've collected should now be seen or redone through new eyes, since everything they've been doing up until then has been potentially falsified by the master.
So, what do you guys think?
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