After beating the game twice (Institute ending and Minutemen ending), and watching the other two on Youtube, I'm left with the following question: How can any "good" character justify going against the Institute?

Your options are:

1. Work with the Institute to make their technology beneficial to the people of the Commonwealth, while taking huge steps to change their image and communicate positively with settlers. Violence is always the last resort.

2. Work with the Minutemen to destroy the Institute because a handful of it's researchers abused their incredible technology, destroying mankind's best hope for a future because the general population doesn't understand it.

3. Claim the Institute's tech for the Brotherhood, who have essentially engaged in a hostile takeover of the wasteland. Bomb the hell out of everyone else to steal their tech.

4. Join the Railroad in their quest to kill lots of real people in exchange for helping out fake people. Take zero responsibility if those fake people go crazy. Kill the real people who create those fake people. Have no further plans for the future.

As the leader of the Institute, your character has the power to utilize all of the organization's technology for the betterment of mankind while simultaneously putting an end to the small number of morally gray experiments they engage in. You could easily create an Institute where Synths have freedom (there are scientists in Robotics who seem to want this even under Father's rule), and where kidnappings (which are already exceedingly rare and conducted only by a small facet of the group) are abolished entirely.

The sad thing is, the average Commonwealth citizen still sees the Institute as evil, largely due to unfounded rumors and exaggerated stories that seem to have all spun out of one or two small-scale tragedies.

Even close allies like Nick and Piper refuse to see the Institute as good, seemingly ignoring the fact that you, their friend/savior/lover, are put in charge of it. These people will only agree with you if you choose to indulge them in their ignorance, burning the equivalent of the Library of Alexandria just because people are suspicious and uninformed.

So again, I'll ask: How can any "good" character justify going against the Institute?

You know a lot of people have argued the Enclave had the means of rebuilding so they should be supported. The ends do not justify the means and the only truly good ending appears to be the minute men. I have not beaten the game and not watched any videos, but a dictator with better tech versus a semi democrat and free group like the minute men. I will pick freedom over tech (even if you end up in charge of a group doing some morally questionable activities, still seems a dictatorship).

The Minutemen are an Army, they are by no means democratic. Did you just say that because they are "good" and therefore must be democratic (spoiler alert, the Enclave actually was a democracy and they were evil).

Enclave is totally different, they were basically post-apocalyptic Nazis.

Even if you become the head of the Institute, the player character is still the General of the Minutemen as well (and Preston is the most understanding of your decision, he trusts that you know what you're doing).

The Minutemen are doing some great small-scale work, and there's no reason why that work can't continue after the Institute ending. The only difference is that you preserve the nuclear reactor that can supply limitless energy and ensure a safe place for humanity's continued existence forever, along with the brightest minds the Commonwealth has to offer. The morally gray elements (Zimmer, the Bioscience head, the head of security and even Father to an extent) are all either dead or under your direct control by the end.

First things first, my work computer wont let me quote so sorry for this.

@ The Enclave - Nowhere was it ever said the Enclave voted for their leaders, their is no lore I can find on Richardson getting voted in and the computer just said I am president come here, so not a democracy. Find me proof beyond they are the decayed remnants of the American government.

@caramel_cod - So if you knock off Hitler and take over Nazi Germany does that make everything not evil that happened. A fair example as the Nazi's did some good before totally going batpoop insane.

Just because you become the head of a questionable society does not immediately make them good or that a good ending.

The minute men are a defense organization that are actually helping people right now, building places for them to live, getting food and water for them and defending them. They are the beginnings of the next great thing in the area, I could see them expanding the way the NCR did with the help of the rangers. Nothing evil about them, they actually just want to rebuild and will start now.

The Nazis weren't a "questionable society," though. They were irredeemably evil and relentlessly violent. The Institute actively avoids violence, and has the most peaceful of all the endings.

http://fallout.wikia.com/wiki/State_of_the_Nation

dike Richardson's notes reminding himself to insert a plug for his re-election into his speech. Pretty indicative that he was elected and intends to run again otherwise such a reminder wouldn't be necessary. It's also mentioned in the Fallout Bible depending on how much stock you put in those. Eden succeeded Richardson via the Presidential Line-of-Succession and simply didn't institute another election, being an amoral abortion of science and all.

So yeah, the Enclave voted for the President.

EDIT: And from the man himself:

Fair enough to Richardson, I stand wrong on that one. Still no votes for Eden though.

Indeed, he was an outlier, resulting from a very difficult predicament for the Enclave, and he became President through emergency procedure. Being a soulless work of evil though he simply decided to not end have another vote.

But at their evilest stage the Enclave was a democratic nation.

The Institute is a slave state. There's not really a way around this other than to drink the Kool-Aid and say, "Synths aren't people." Which is a difficult prospect to get around given that Synths are people enough to run away from the Institute, talk amongst themselves, be terrified of having their memories erased, and produce people like Nick Valentine.

Hell, Codsworth and Currie seem to be sentient but that might be because they've had 200 years to grow and have avoided being insane.

The Institute can't really be separated from its slavery either as all of the humans in the Institute are researchers and scientists who leave the grunt work to the Synths. You can't switch over to manual labor and free the Synths without presumably all the upheaval removing slavery from a slave-based economy will. There's also the fact the Institute isn't a cuddly organization if you bother getting Valentine's approval high enough as his stories are pretty badly-needed information about the history of the Commonwealth.

The Commonwealth isn't the Capiatl Wasteland and actually managed to produce something like NCR twenty-years-ago. The Institute destroyed that with their use of infiltrator Synths and killed all of the representatives there. They're also probably responsible for the Minutemen's destruction.

All to maintain power.

A lot of people point out that the "isolated experiments" by a handful of researchers is an issue but most of the kidnapping subjects aren't brought into the Institute as guests. No, they're brought in as test subjects and the FEV experiments are why the Commonwealth is overrun with the Institute. Any sympathy for the Institute I had goes out the window when I realize the Super-Mutants and their mass-murder is all the Institute's doing.

As for the Minutemen, they're not an army, or more precisely they're not JUST an army. They're an army which works hand-in-hand with the Settlements they protect. They don't rule the settlements they protect but they assist them and receive assistance in return.

Maybe not formally, but the fact that you can build whatever you want in their settlements, handle all the defenses, tell them what to do and bring settlers there shows that Minutemen are more than just protectors. And such amount of power WILL eventually make them more assertive.

This reminds me of the Star Trek episode where a Federation anthropologist recreated the Nazi party on a contacted world because he thought they needed order and that the Nazis had that and as Furor he could control the party so that it did good. It didn't work out.

For the people who have made it to the end, what faction did you choose and how did the ending work out? What did you think?

To be fair, the issue is the Settlements are mostly places you've constructed yourself. The settlements who support you are, theoretically, a different story.

But no, no one is standing up to the New Guy in ChargeTM either.

I went with the Minutemen. They were the first option presented to me, and it feels damn good to be the General. The one thing I always wanted to ask at the Institute was about the kidnappings, and replacements. A random encounter I had greatly influenced my decision. I had seen two identical men. One was on the ground, the other had a gun pointed at him. The one on the ground was talking about his wife, and his children, and how he loves them. The one pointing the gun said he was a synth. I had no idea which was the Synth at first. Why wouldn't the Synth try to kill the other one? Because it wants to blend in. Either way, the Synth will die. The challenge was figuring out which one was lying. I couldn't, so I took a gut feeling and winged the one on the ground. It was the synth. The one who acted innocent, and helpless was the Synth.

The machine was built, and designed specifically to assassinate, and replace that man. If that isn't evil, then I don't know what is.

If you actually play the Institute quests you'd see why they "kidnap" people when in actuality they don't kidnap them at all. If the synth was trying to kill him, why would he be on the ground begging for his life?

The Institute does different people with different people.

Some of them are just pure evil like FEV experiments.

The Institute also replaced a father with orders for said father to kill his family after a period of observing them.

The Institute has many noble, wise, and redeemable qualities.

Ignoring their utter amorality in the pursuit of science, however, is a mistake.

Now, that doesn't mean you SHOULDN'T side with them.

Because as the head of the Institute you could reform it or end slavery or any number of things.

But the status quo is pretty awful.

I dont know i like how the new BoS is more of thier own agenda, but they still care about the ppl.

For me the good choice was the BoS. Minumen since they want to have a Free boston but i think they dont have the power to control it.