I've played through most of the main story and read through a few posts in the forums but I still have some unanswered questions (it's entirely possible that I missed something).

After going to the institute, I was disappointed in how few questions you can actually ask. It felt more like a sales pitch - I wasn't able to ask about the reasons people hate the institute.

Why do they send robots to kill people? - after doing a few institute quests, they make it sound like the only reason they leave is to bring back runaway synths, yet there are multiple areas throughout the game infested with gen 1 synth that clearly were sent there to clear the place out.

Why are there body doubles? I've come across a couple events in game where this was brought up including two identical guys in a standoff. I was able to charisma my way into finding out one was actually a synth... is that something the institute did or was that a runaway synth who picked that person to replace?

Even now when I'm friendly with the institute (haven't made the final decisions yet), why do they send synths to attack my settlements? They're friendly when I get there, but slaughtering my people.... what is their motivation for that?

Basically, if the institute just wants to keep to themselves in their little underground hideout, why are they killing people on the surface? There has been 0 explanation for that as far as I can tell.

The short version is the Institute believes outsiders and Surface Dwellers can't be trusted and can only be dealt with from a position of control. They created Synths to serve as their Sleeper Agents, Spies, and Replacements to control the Commonwealth in secret.

To understand this, you actually need to talk to Nick Valentine and others.

The Institute doesn't want you to think they're, well, EVIL.

They also kidnap people as experimental test subjects because they need bodies to experiment on. They replace these people with Synths to make it seem like no one has been kidnapped, unaware this makes people EVEN MORE PARANOID.

Basically, they're the Illuminati with a healthy dash of "Invasion of the Body Snatchers."

As for why Synths are attacking, that's probably because you're also allied with the Railroad and Synths have orders to destroy sympathizers with them.

I guess that makes sense - I just wasn't sure I could believe outside people since they could be just hearing rumors - I wanted to get some straight answers from the source - which doesn't seem like it's going to happen.

Well, then basically I don't want to pick any of the factions.

The brotherhood I guess is the best choice because at least they aren't doing evil things.

The railroad has good intentions, but they don't have to power to actually change anything major.

The minutemen are good for small-scale things, but they aren't going to come together to do anything major, either.

The institute has the power to change everything, but they aren't going to use it....... if you side with them, can you force them to actually help the commonwealth?

I don't want to side with them, but destroying them and all their tech doesn't help anybody either............... ugh....

Each of the factions has its own downside and upside.

The Brotherhood of Steel is going to conquer the Commonwealth, eliminate all nonhumans (ghouls, Synths, and Super Mutants), then rule as feudal overlords. The thing is, the Brotherhood is GOOD AT THAT and as while its racist as hell for Goodneighbor and poor Nick, it's not like the majority of Super Mutants don't have it coming in the Commonwealth being murder cannibals.

You can also join the BoS if you're pure human.

The Institute will name you as Director if you choose to support them as they're sick and tired of making vast improvements in science with no gain for the outside world. They're academics and don't know how to run a military or command a nation. Shaun says, as a Pre-War lawyer or soldier, you're one of the few people qualified and the Institute quest-line is your "audition."

If you're willing to have both Piper and Nick hate you (though Piper can be blinded by love if you romance her) then you can headcanon as head of the Institute that you can liberate the Synths and replace them with dumber robots.

Maybe also use your tech to be the new House.

If you side with the Railroad then you destroy both the Institute AND the Brotherhood of Steel but that doesn't noticeably improve the Wasteland. Well, except for the fact the Institute is the reason that the Commonwealth didn't form a new NCR. It turns out that 20 years ago, the Institute prevented all of the settlers and the Minutemen from hashing out a mutual defense and trade treaty which would also unite them into a nation.

Nice job, Shaun. Real nice.

The Minutemen actually have potential for long term gain but only if you REALLY REALLY GRIND THEM. If you get over eight settlements and five artillery, you become powerful enough to defeat the Brotherhood of Steel/Institute and form the nation which was prevented from happening 20 years ago. It'll be decades before it's up to NCR's level but if you evacuate the Institute before destroying it, that means all of those scientists are suddenly out in the wild using their knowledge for the common good,

It gets better if you ally the Minutemen with the Railroad in the Hybrid ending as the Minutemen are now allied with all liberated Synths who agree to help you rebuild the world.

The Brotherhood wants to cleanse the Commonwealth of nonhumans. Pretty sinister. And yes you should complete the Institute quest line because in the end, they do whatever the [censored] you want them to.

To be fair, Elder Lyons showed us what happened with trying to reform a society wholesale.

That sounds like the true good ending I guess....... but is a world without an airship a world worth living in?

I'll be honest, Bethesda was really assholish about this.

There's kids on the Prydwen.

What the hell, Bethesda?

And what the hell Maxson?

Also, it seems weird that siding with the minutemen you would destroy the brotherhood. I went through both sides' quests and they never even mention each other. They definitely don't mention hating each other. If you side with the BoS, you don't destroy the minutemen.... why would the minutemen destroy the brotherhood??

Because the Minutemen stay a tiny irrelevant faction if you do another ending, sort of a subsidiary of the faction you side with. If the minutedudes wanna take over the Commonwealth, of course the Bros need to be destroyed.

You don't have to with the Minutemen but if you're allies with the Railroad, yes.

Also, the Minutemen would want the BoS destroyed for all of the ghouls in their settlements.

If I just go back to doing sidequests surely they'll all get together and sort things out themselves, right?

Like the Stormcloaks and Empire, you can safely ignore them forever.

It's not like you get ending slides either way.

True, but its not to say that Institute reform is impossible.

There's good people in the Institute. They're just often blinded by desire for unhindered scientific development and progress. I think the best possible ending is a good-karma SS who's both Director of the Institute, and General of the Minutemen, and able to bridge the two worlds.

Apparently Piper will admit that the Institute might be a good choice after all if you take her on the Institute quests. Specifically the Courser one to hunt down the raider synth.

Not sure about Nick though. I doubt he'd ever accept the Institute.

I mean there was undoubtedly kids in Raven Rock in Fallout 3 too. And Prime blew that right up.

Enclave soldiers don't just spring out of holes in the ground.