#they'd always want the Institute gone just cause too much tech but synths??? Thats a result of Commonwealth paranoia

[theology101]

The Brotherhood of Steel don't commit Genocide

Their goal is to protect humanity - not including Ghouls - from Dangerous Technology (Laser weapons, FEV, Replication tech) and try to destroy the fruits of that danger.

But they're not the Enclave. They're not out here trying to make a Human Ethnostate.

As a rule, they've given it a go once or twice but, typically, they're not genocidal. Does the Brotherhood of Steel dislike Ghouls and Super Mutants? Absolutely. Did the West Coast chapter care that the NCR allowed both to be citizens? No, they didn't. Because they weren't a danger to Humanity as individuals.

Why haven't they wiped out Goodneighbor in Fallout 4? Or hell, why doesn't MacCready (who isn't the BOS biggest fan) bring up Underworld or any Brotherhood activity there? No, he doesn't - so its safe to assume that they weren't wiped out.

In Fallout 4, the fight is against Synths the same way it was about Super Mutants in Fallout og - the Synth is just the dangerous byproduct of the Brotherhood's actual target, the Insitute. Just like how the Brotherhood wasn't out to kill all Super Mutants, but the Super Mutants who served the master and threatened Mankind.

From Maxson's perspective (wrong as it may be), he thinks that Synths represent a danger to mankind for two reasons:

They have the ability to near perfectly infiltrate any organization with sleeper cells that can be activated at a moment

Synths might one day decide that they don't need Humans anymore, and instead of trying to run away from the Insitute they'll take over and mass produce

Both of these are nightmare scenarios for the Brotherhood. But the second the Institute is gone, so are both of those points. There will be no more infiltrating (except for DiMa's shenanigans) and the ability to make new Synths has exploded. And, actually, so too did the way to make new Super Mutants so once the current batch is gone there won't be anymore.

Arthur Maxson's work here is done. Now he'll just set up a new local chapter (he has the ego to just unilaterally make one, or he could have made contact with the West Coast and got permission) in Boston. The Brotherhood doesn't want to be the local government, so they'll let the Minutemen do that but they'd mostly just be here to vibe.

Shit, they can't even do anything about the Synths. Not even a deep brain scan will reveal if there is a Synth component, and its impractical to do mass-brain surgery. The Brotherhood pretty much has to wipe their hands and go "we did good gang"

So sorry Thaddeus, no we will not be "killing all the ghouls" because, to be completely honest, there are more important uses of the Brotherhood's time and micro-fusion cells.