[spoiler WARNING]

After going through the emotionally tumultuous act of killing off both the Brotherhood of Steel and the Railroad all for the sake of my character's son... and becoming the new director of the Institute, why are my settlements still getting attacked by settlers who turn out to be synths. The SRB is the worst run branch of the institute.

Perhaps Bethesda would consider a DLC with a mission where the player gets to kidnap and replace Justin Ayo with a synth as a way of stopping this kind of thing from happening.

Had I known before it was too late, I would've replaced him. Now I'm stuck with that knob, talking down to me and sending me to see Mayor McCheese in Diamond City. I have REAL stuff I need to be doing Justin.

Mayor McCheese XD lmao

He is a smug bastard.

As a side note, the quest defend settlement quest also doesn't seem to update properly after you finish it.

Maybe a Logical Problem from Bethesda Side, or just a Bug? The Informations why and for what they attack the Settlements are non-existent. So long the Player gets Boom-Boom Gun Action. Father said ones they only attack People who interrupt their Plans, but what Plans i interrupt when i do only a Settlement on Sanctuary? Bethesda made a few Logical Bugs/Problems here.

That's just how the Institute rolls, dude.

You gotta get on with the business or resign.

Boy, was shooting that bag of useless mud in the face satisfying.

AD VICTORIUM!

You know you can replace him as Division Head of SRB in the course of a particular Institute quest right?

Anyway, Justin Ayo is actually pretty complimentary if you just ignore his quest to get a message from the Synth-Mayor. He applauds your actions in Libertalia and compliments you on your combat skills.

The Diamond City Courier quest just seems to be a hold-over from when you weren't Director honestly.

But yes, he's pretty much the only one in The Institute that doesn't bow down and kiss your feet after becoming Director. With the possible exception of Higgs (although he begrudging admits he was wrong).

Edit: Regarding the Synth-attacking settlements thing. That appears to just be an oversight on Bethesda's part. Hopefully they'll fix it in a patch or, more than likely, a mod will eventually. I've only run into like once throughout my entire playthrough though.

I really wish Bethesda gave radiant quest npcs just one or two different lines to utter after the main quest... It's the same with Knight Rhys, you can go talk to him after becoming Sentinel and he'll genuinely apologize for his attitude and act very respectful, but accept the radiant quest he still offers and it's back to 'don't show your face here until that location is clear, understood?' in the same breath. Honestly, it doesn't seem like it would be a huge effort or a costly addition, and it would go a long way towards making the game more immersive.

Also, can someone please tell McDonough I'm Director now and he should really make time for me, busy Mayor or not? The Gen-1's in the Market recognize me, but not the main infiltrator? And before all that, did no one think that voice on the radio sounded familiar?

Yeah Bethesda games have always been [censored] about this sort of thing. And its annoying every time.

I saved the world in Skyrim, am a Legate in the Imperial Legion, and Arch-Mage of the College of Winterhold and random guards still mock me about my sweet-rolls.

You can't replace him once you've become Director. As soon as you complete or fail "Tradecraft" you can't do the quest to replace him anymore.