Morality in video games is an often attempted subject but is almost always done in a ham-fisted and incompetent way, the best way I have seen morality tackled in video games would be for the player to treat the avatar like a person and the non-player characters as persons as well. Doing morality like this introduces a complex system of how many people did I kill how many are innocent and how many could I have avoided, especially in a game with a “Dumb AI” like Fallout.
So let’s tackle the external conflict of Fallout 4. Now on the surface, it’s clear you want your kid back. But at a more in-depth examination we see flaws in this hasty reasoning and surface level examination. For one your “Child” is not a child Shaun has grown up and now runs the institute as “Father” now the question becomes not can I get my kid back but can I accept my child even after he has done demonstrably horrible things in the name of progress. This is not a handled well in game leading to a simple set of speech checks, but when we examine it outside of the game we can spend hours trying to understand the conflict of accepting a child that has done horrible things, kidnappings, murder, espionage, and extortion just to name a few. There is also a huge number of other external conflicts throughout the game that become internal conflicts if you consider the personhood of the NPC. Killing waves of nameless cannon fodder becomes more difficult if you give them all names, and upon further examination of fallout lore even killing super mutants becomes problematic these are just people that were experimented on without their consent, who am I to kill these innocents. Even ghouls have tragic backstories if you take the time to read terminal entries.
What I am really trying to say is the distinction between internal and external conflict becomes more and more blurred if we consider the personhood of everyone we kill. At a certain point the model of go here kill these dudes and move on becomes unsustainable, what a normal play through of fallout looks like to the NPC is a genocidal maniac going around and killing everyone who dresses slightly different than them, and talks in a strange way.