This entire questline is a disaster of nonsense. Every single character – including the player – has to behave irrationally or jump to ridiculous conclusions for it to work.
Shaun decides to wake up his parent and turn them loose in a mad world of violence and horror, under the assumption that you would somehow reach him and no die horribly to the first raider or supermutant you meet. Why would he not simply bring you to the institute? Barring that, why not leave supplies and a note?
Nick makes nonsensical leaps of logic to send you after Kellogg. Kellogg’s hardware needs to magically survive regardless of the fact that he very likely died in a nuclear explosion. Your character needs to reach into his skull and pull out those bits, despite having NO REASON to do so.
Nick needs to come to the absurd conclusion to scan a dead brain without knowing about the hardware you recovered. Then Nick also needs to look at the little gizmo and conclude that Doc Amari can make it work.
Kellogg is evidently babysitting a robot of the leader of the Institute, despite the fact that there’s no reason to give him that kind of job and the only reason he did it was so the writer could mislead you into thinking Shaun was 12. The same goes for the fact that Kellogg evidently never aged and called two different people “The Old Man”.
Then when you finally reach The Institute, Shaun leaves out a robo-clone of himself for you to find, for no discernible reason other than to further traumatize and confuse his parent.
We could maybe forgive the brain-scan nonsense if that was one of many routes into the institute. If the developers had the stealth route, the combat route, the charisma route, and this thing with the brain-scan was the science route, then we might be able to gloss over some of these problems. But this is the one and only route that the story can take. Every character must go through this. There’s no complex branching or fail states or alternate outcomes. It’s not like the quest needs to accommodate different character classes or having the quest continue with key NPCs dead. This is a perfectly linear story, as simple and chronological as a Naughty Dog game.
Laying aside that fact that it’s pretty outrageous to build a Fallout roleplaying game around something so inflexible, there’s just no excuse for why this story can’t make sense. If you’re not going to branch or offer player choice, then the least you can do is make sure our one-and-only option feels like a natural progression of a story and not a horrible series of blatant contrivances and lazy hand-waves.
We’re heading into the endgame now. The mood isn’t likely to improve anytime soon. Buckle up.