part 2 can be found here, ages ago just before my card went AWOL.
Hieronymous was going to follow through the story but not join The Minutemen. There are four factions to choose allegiances with. The Brotherhood of Steel are the militaristic assholes all about technology and a for-your-own-good sense of violent superiority. The Institute is an underground bunker of descendants of old world scientists, who make robots with laser guns and have a creepy agenda involving replicants & replacing people. The Railroad is directly against The Institute acting as liberator of the intelligent synthetic humans, identifying them as sentient and smuggling them out into The Commonwealth. They're a bit fanatic but have their hearts in the right place. The Commonwealth doesn't care much for them And I already mentioned The Minutemen, who really only exist to populate and protect The Commonwealth. They're the Good Guys if a bit short sighted.
The only way for the Railroad to accomplish their goals is for the Institute to fall. And they know I am motivated to get into the hidden base, so they help me. They gain my loyalty through a number of liberation and combat missions, basically working me into being one of their "heavies" -- well armed and armoured soldiers taking out their enemies and protecting their liberated synths.
Meanwhile I am doing my best to NOT get caught up in the support of the settlers and their little towns, but once I liberate one, I feel a bit protective of it. No, I am not back in the Minutemen, but these are my people and keeping them flush in armour and weapons is not a bad thing. Oh the time you can waste just upgrading weapons and armour. Take every last thing off a fallen enemy, quick travel back to the town that is in need, cover everybody in Combat Armor and automatic lasers and head out again. Again with the false sense of accomplishment and benevolence.
And your son is there. But he's 65 and he's running the place. You see, back when that mercenary killed your wife and took your baby son, he was already working for the Institute and their previous leader. They needed clean DNA for their experiments and a cryo'd baby was perfect. You and your wife were collateral damage. When you come across the same mercenary, after you get out, it's a smoke & mirrors game. His life has been extended and your son was raised in the Institute the entire time. In fact, your son Shaun is the one who allowed you to be released all these years later, as he needs a trustworthy contact on the surface now that the mercenary who killed his mother had become unreliable. Your son's a bit of a dick. And you gather this very quickly, but since you are now working for the Railroad, you pretend to go along with Shaun's agenda to find out what their end goal is AND help out the Railroad.
This is where the story becomes a bit muddled. You know you are being manipulated on both sides. You know Shaun has a creepy agenda and you begin to suspect he knows you are playing both sides. But that's fine, he's OK with that. As long as you accomplish his murdery goals, killing non-Railroad bad guys for him and gathering up stuff he needs, it's fine. You are his gun and you cannot help but defer a bit to your own, albeit aged, son. And he is directing you towards becoming the new leader of the Institute so maybe you can mould their agenda to your own, a less homicidally superior one.
Its very weird. Heroism is being left to the wayside as you become a pawn in two major powers' games. The Railroad is looking less and less benevolent and more just about kicking the ass of the other power they don't like. The Institute could complete their goals without murdering The Commonwealth but they don't want to. Meanwhile I made friends with the Brotherhood, but didn't follow their missions for long as I was lead to a big climactic battle at a small settlement called Bunker Hill. All three factions take on each other there, and the average Commonwealth people are all collateral damage. Seriously, even the Railroad shoots anyone who doesn't stand with them. But I am playing the long game now, still doing what I can to play both sides until I determine who the real bad guy is. Or I am just forced to take a side because I have to be committed to something.
The game ends (???) with a new radioactive hole in Boston. The Institute is dead, but many escaped. The Railroad released hundreds of synths before they blew up the place but the Commonwealth still doesn't trust synths. There will always be a Railroad leading them to safety and protecting them. And the Brotherhood? Well, you had to murder them all so they wouldn't get in your way. I was killing people my character had made friends with, had drinks with, patched up my armor with. As a player, I was feeling pretty low by the end of the game.
At the end of the game, you are nobody's hero. You are the MurderHobo, the guy who had no home but wandered everywhere killing anyone who got in his way, friends or foes. You took their stuff, you garnered experience points from them and you bank your gold (bottle caps). Its not as fun as the D&D players made it out to be. You told yourself you were there to be the hero, that each death was for a cause, a just cause. But in the end you only did what you were best at -- kill.