A video game story sounds like a total nightmare to craft. Not only do writers have to compensate for the fact that a game can last for tens of hours - alongside the need to incorporate side quests just as big as the main narrative - but the changing nature of production can mean levels and missions are altered or ripped out at the last minute.
All of this falls back on the one element that should be set in stone: The story.
It's the kind of environment that led to a whole rewrite of Destiny's story when the studio was half a year out from release, so it's no surprise that even the best video game stories don't always tie everything up in the neatest of ways. Especially when developers are tasked with telling a cohesive narrative over an entire series, plot threads are likely to be introduced that never come into play in the major way fans expected them to, or whole characters are just dropped because they're no longer relevant to a story's new direction.
That doesn't make these games bad - and it sometimes doesn't even make the story weaker - but it can still be baffling to look back at some releases and identify major plot points that went absolutely nowhere.