Credit where credit is due on the big twist of Fallout 4; the reveal that Shaun is the now-elderly director of the Institute comes part and parcel with the realization that with the death of Kellogg- who, as it turns out, was basically turned over to you as an olive branch- the institute is now completely free of anyone who has actually wronged you personally; your straightforward, no-further-justification-needed revenge quest has been cut off at the knees. Which does, in fact, clear the way for you to evaluate The Institute as it actually currently exists and not as the amorphous boogeyman you were planning on John Wicking as little as five minutes ago; if you stand against them it's going to have to be on general principle, based on what they've done to others, and on the flip side a sufficiently amoral character, absent the roadblock of a personal umbrage, is completely in the clear to throw in with them for comfort and power. They did not square the circle on this because they cannot square the circle on anything. But in the abstract it's a pretty clever piece of storytelling- where are you going to direct that narrative-propelling righteous anger when it turns out that institutional turnover has beaten you to the punch? Were you ever actually angry at the machine, or just at the specific cogs? Are you playing as the kind of person who thinks that there's a difference?