Doesn't matter if you quit at the chemical assault-part, just because one person abandons them, that probalby would not stop their plan in the long run. You won't prevent anything, just delay it at best. They will thank you for your cooperation and your work. You were useful.
The way you can aim to actually stop them, is by joining FD. That way you're not just looking the other way when they mutanize the public, but can fight against the idea with all your might. And that would probably better for your conciousness.
Oppressive government is bad and once it stabilized, it's very hard to overthrow it. If robbing the train prevents this or at least slows the process, it's something seemingly evil acted upon basically innocent passangers - in order to avoid an even greater catastrophy that could potentially ruin a lot more lives.
With that said, groups like the FD draws in a lot of anarchistic characters that see this as an oppurtunity to freely act violent and be supported in it. Folks that are only in it to raise hell and would do it in a civilized culture as well. At least here, their energy is channeled towards an even greater enemy of society that is an organized, well oiled, methodic and works very much counciously on the erradication of humanity.
FD higher-ups should be aware that their group is nowhere near as the rebels in Star Wars for example, but more like rejects of society and criminal scum that would never fit into the future what the Protectorate plans for the world (wheter the world likes it or not) and now have refuge and supplies among the FD and a place they feel like they belong. As long as they're happy that is as it would be foolish to completely rely or trust these bunch. Or expect any loyalty from most of them when the tides are turning.
I never met FD yet as I'm still at an early part of the game, but the way I see it, reading these posts, FD is made up of Neutral Evil and Chaotic Neutral characters as their footsoldiers. Chaotic Goods would gladly take justice in their hands and show voilence against evil, but would probalby not be okay with methods that involve harming innocents. While their leaders are probalby True Neutrals that value their independency more than anything and would rather die and sacrifice others then fall under the rule of an oppressing government.
As for the Protectorate, they are Lawful Evils. Would happily turn people into mutants if that leads them to more power and as long as they can do it while crafting laws to support them, especially being portrayed as the protectors of civilisation, they won't have any second thought. They see FD as a bunch of criminals that worth more as mutants than the human garbage they are and are perfectly consistent about generally thinking that some people just doesn't worth the air they breathe and they're doing just work by eliminating them. Making the world a better, safer, cleaner place. And might as well take their land to further their own prosperity.
So based on this thread so far, I'm going to side with the FD. I have a feeling that I might meet more a$$h*les within the Protectorate and I sure as hell don't want to work under them. Should I meet some decent bloke among the Protectorate, that might probably be a naive fool that did not open his/her eyes yet and probably just being used by them the way they would exploit my character too should I join their side. While I really look forward to see a likeable fellow over at FD.
Some might have valid reasons to fight against the Protectorate (possibly past tragedies causd by them), while I can't imagine that the expansion and mutanization of the Protectorate can be justified. Also, approaching this conflict from FD's side seems more interesting.
