Fallout 4 Far Harbor: Tell Commonwealth Factions

Informing the Brotherhood, Institute, and Railroad

Upon learning of a Synth Refuge (Acadia), your character gets the option to inform either the Institute, Brotherhood, or Railroad. Given the importance of the leader of Acadia to the storyline, this will undoubtely change things and is likely something you'd rather do later into the DLC or during a second playthrough. But if you're roleplaying a true Brotherhood Paladin, then perhaps you'd like to make sure those abomination Synths do not get to thrive in a human world.

When Will they Arrive
None of these options has any bearing until you complete enough of the main quest. No matter how long you wait the Institute or Brotherhood will not show up and attack Acadia until you've made it far enough in the Far Harbor story. If you do this, you'll lock in that choice, and that faction will then have a presence on the island.

They trigger as the fifth quest, after securing DiMA's memories and finding his secrets, and confronting whomever (it's seemingly after The Way Life Should Be) so they will not block you from investigating and you may indeed override them by making certain choices. By doing this you are choosing to not solve the Island's problems yourself, at least in regards to Acadia. Though the game may let you, I should warn you that if you take the option to tell them AFTER you've dealt with the Island's problems, the Institute or Brotherhood may show up but NPCs may be made essential to the point you cannot complete the quest.

Inform the Railroad

Who to Tell: Boxer

Of the three options, informing the Railroad seems most tame, and if you inform the Railroad you can still inform one other faction. Because of these things, I'm mentioning this first. You do NOT get a quest from informing the Railroad about the Synth Refuge. Boxer says she'll go there as soon as she has time, so it's a stall for when you get to the proper point in the main quest.

I don't yet know what happens with this one, but will write more when I do. Would appreciate anyone who has done it sharing the info on the comments at the bottom of the page.

Inform the Brotherhood: Search and Detroy Quest

Who to Tell: Lancer Captain Kells

At the point it occurs, the Brotherhood will do what the Brotherhood do - your quest will be Search and Destroy, and you'll work with the Brotherhood to remove the Synth outpost of Acadia. This prevents you working with or against DiMA to change the fate of the Island and may keep it in a state of war between CoA and Far Harbor, at least to my current knowledge.

Inform the Institute: Forbidden Knowledge Quest

Who to Tell: William Mosley in Advanced Systems

You will get the quest Forbidden Knowledge to subdue the Synths of Acadia and return them to the Institute. This is less aggressive than the brotherhood option, but has the same outcome in terms of dealing with the Island's problems.

Someone on steam forums reported that if you are stuck in the Forbidden Knowledge quest you can try killing the Synth with the quest marker last and that the quest may complete properly.

Informing is an Alternate Ending

So, informing the two aggressive factions (institute/brotherhood) is an alternate ending for the DLC. It allows you to show your loyalty to the faction you're working for, basically for roleplaying purposes. These factions would not have a role in the DLC without these options, so it's cool that Bethesda threw them in. I recommend against the last two, but again don't know what Railroad does for Acadia. Overall by doing this you may be missing out on some decent rewards. Definitely consider finding all of DiMA's secrets before you complete the Best Left Forgotten Quest so that you can at least get those rewards.