And basically thats exactly what happened.

The in-game screen transitions mention that the Institute used to work more closely with the people of the Commonwealth, but cut off contact after mistrust was sowed between the two for various reasons.

And in addition, the reason the Institute scientists needed Shaun, was because most of the Institute's DNA had been altered by surface radiation. Suggesting that at some point in the past, the Institute worked regularly above ground, which is whats causing the damaged genes to be passed down to the current generation of Institute scientists.

So yeah, the explanation is already there. You just need to pay attention to details.

hmmm you could always go the revenge way I mean your whole entire life is destroyed, both your child and spouse are taken away from you. Even if father was your son, he is no longer Your BABY.

Well, Smileomaniac, all of your problems seem to boil down a complete rejection of the Institute being not only advanced to the point of being not only able to have a large facility underground (which isn't that difficult given Vault Tech and the US government made massive numbers of such tunnels which the Institute could easily convert--not to mention such places in RL) but that they don't suffer any scarcity of resources.

Which is the Institute's entire thing.

That they're a fully functioning Rapture-esque society built on robot labor. A pocket science utopia in the Wasteland.

But yes, if you don't believe the Synths are slaves then the Railroad's view will make sense and the Institute is a bunch of good guys. Also, if they DID spell it out, there wouldn't be any ambiguity would there?

I don't think there is but I don't reject the idea of machine sapience out of hand because they're not made of blood and skin. I also think Ghouls are people too and exist in pretty huge numbers on a per capita basis.

There's no "good" guys and "bad" guys in Fallout 4. Whatever faction you choose, depends on your morals and whatever you believe is right/wrong.

I believe the Railroad is the most morally right out of all the factions, the Institute has enough brains to progress humanity out of the dark ages it's currently in, and the Brotherhood has been built upon enough discipline to maintain order that's greatly needed in the Wasteland.

I always side with the Brotherhood because without the Institute, there is no higher control of Synths and no real purpose for the Railroad. Regarding the issue of android bias, Danse was right under the Brotherhood's noses for the longest time and they hadn't any idea until the SS retrieves data from the Institute. I love Danse, but if the Institute regained control of him for even a brief second, he could have easily been reprogrammed to sabotage the Prydwen and assassinate Elder Maxson. The Institute fed into fear mongering for too long, they'll eventually meet their inevitable end with the deceit that goes on within the ranks. Even if the Brotherhood isn't noble, they're at least honest for the most part.

Oh, in one of the Railroad quests, there's a terminal at MIT (of course) which says they've requested massive funding from the government to work on an underground project.

So, yes, the Institute predates the Great War.

All I know, is that the minute men (and women) are the most morally right (and responsible) faction. They try to do right by the Commonwealth. Although, joining them (becoming general) as a female SS makes no logical sense (until you get some combat/survival experience).

She says, "Dust off that law degree" which implies she hasn't used it in a while.

I'm inclined to think she was either conscripted to the military or joined voluntarily TO FIGHT COMMUNISTS.

first, I love the fact that there is no clear cut good guy, very fun to have these discussions.

now, the thing I'm trying to do is figure out who will actually last long enough and be strong enough to change anything. the railroad goes out the window as they are a small faction with a very specific goal that once concluded leaves everyone right where they left off, struggling to survive in the wasteland.

the minutemen are tricky because while it is incredibly relevant and realistic in its goals its ripe for falling apart and politics much like already happened to it. short term its viable with you in charge, long term I'm not so sure.

that really leaves the institute and the brotherhood for me. the brotherhood is very much a blunt instrument but simply getting rid of everything that's "bad" wont backfire. the institute seems like its playing with fire with the amount of tech they are working with.

Actually, it's good to talk to Valentine as his friendship really blew me away with some details which should have been in the main quest.

1. The Commonwealth actually formed something like NCR - "The Commonwealth Allied Settlements" (CAS) and they had a big meeting to hash out their new government -- which the Institute killed all the representatives of and started a war between them using Synths.

2. The Institute may have been responsible for the Minutemen's decline as they've been sabotaging every group which tries to rebuild the Commonwealth except them.

They are ENORMOUS hypocrites.

Likewise, the Railroad actually finishes the two worst problems of the Commonwealth by taking down the Institute and BoS. Without them, there's nothing keeping the Wasteland from rebuilding on its own.

It's not like the Capital Wasteland where it's barely holding onto survival.

I wonder if they are the ones hiring the Talon Company and Littlehorn&Associates to keep the Capital Wasteland in anarchy as well. Well, in past wondered if the Institute was responsible for them, but at the time I thought the Institute was a public faction, not a secret society.

Zimmer seemed a bit open about info on the Institute so I think Bethesda wrote the whole secret society thing later

Albeit, the Railroad is pretty open as well.

From what I can tell, siding with the BOS gets you the most unique items as the vendor on the Prydwen sells unique items depending on your rank, and you get the jetpack upon beating the story with them

Nothing to indicate that she joined the military, however. If you look at the army fatigues as a female character (in the beginning) she says that she is 'proud of him' indicating that the male is the only one of the family to join the military. Could be she learned to fight from her husband, or it is just a gameplay thing.

Even in the 'Hi Honey' holotape, it is always the husband mentioned as having military experience. I think that the 'dusting off the law degree' thing is just there for flavor, to remind the player that the female SS was a lawyer, not a soldier.

Besides, it is mostly the first time, when you are first offered the position. after a while in the wasteland, anything makes sense as there is now experience no matter the protagonist's original skillset.