Honestly , the only logically consistent decision to make in the game ' s plot is to side with the Institute and the Minutemen . Unfortunately , Bethesda really messed up the overall story in FALLOUT 4 and it really pigeon holed the logic of the plot into a very specific direction . In all the previous games you ' re playing as a mostly blank slate character who can be seen going either way by the end of the game due to the experiences you have and the things that motivate you during your gameplay . But in FO 4 you ' re not a blank slate by any means . Your character is given a very specific backstory and a very specific motivation . The only thing that matters to your character according to the plot and the dialog is finding your son , which makes sense given your characters backstory . But as a player you can totally ignore this motivation and just go around the wasteland building settlements and collecting rare loot for fun . It ' s rather annoying that when you ' re just trying to have fun your character can ' t go through more than three lines of dialog without telling someone about how all he cares about is finding his son , because that motivation isn ' t necessarily your motivation as the player . And it ' s clear Bethesda expects you to care about finding your son and wants to you see that this is the most important thing in your character ' s life , because your characters choice to join any of the factions in the Commonwealth is seen as nothing more than a means to an end . Your character doesn ' t join the BOS because he likes the military lifestyle , he does it as a means to finding his son . You don ' t join the Railroad because you ' ve got a soft spot for synths , it ' s just a means to finding your son . Everything is just a means to an end , a way to get inside the Institute . So once you ' ve found your son and you realize the Institute isn ' t exactly the evil entity you ' ve been led to believe , and the most important thing in the universe which was your character ' s only motivation in life has finally been found , why would you turn against him ? It doesn ' t make any sense . It ' s the science fiction equivalent of hunting down your long lost child only to disown him upon learning he ' s a Republican because you ' re a Democrat . Your character would never turn on your son after hunting for him so long and having lost him so relatively recently . But your character might if you choose to based solely on nothing more than you think it would be cool to play as a certain faction , which even that ends up being totally pointless because all the endings are relatively the same . Siding with the Institute is the only logical decision to make given the story which Bethesda has written you into .