As the story is presented in the original game, the first two routes ("Endings") don't give much context beyond an alien-created machine army conquering Earth, humanity fleeing to the Moon, and the PCs (2B and 9S) being soldiers in the war to reclaim Earth. As YoRHa they strive to keep their emotions to a minimum and carry out their tasks with mechanical efficiency, to the point 2B's catchphrase is "Emotions are prohibited." Further, the machines are cast as all nothing but mindless automatons carrying out their programming; excepting those not linked to their network everybody treats them as just fodder.
Then you get a bunch of whammies that recontextualize everything:
- Having assimilated a lot of data on humans into their network, the machines have become for most intents and purposes human other than their mechanical bodies.
- YoRHa units are made using repurposed machine cores, so they're effectively the same.
- Both the aliens and humans the two factions fight on behalf of are extinct (the machines turned on their creators when they realized they had no use for them, while humanity went extinct as a result of what happened in the original NieR; there's nothing on the Lunar Base except an incomplete human genome and a propaganda center).
- 2B is actually 2E (Executioner), created to kill 9S whenever he gets too close to the truth about the war and has done so several times before. (The "A" Ending has her strangling him to death and hinting at this while she does so.)
- The war is designed to be unwinnable on both ends.
- In the event YoRHa gains an edge over the machines, there's a backdoor into their orbital Bunker that allows them all to be infected with a Logic Virus that will effectively turn them into zombies.
... but most if not all of that interesting information is locked behind hours of gameplay, requiring a runthrough of the same story twice from different perspectives. However once you do that you learn the YoRHa units are
far from emotionless as the above revelations take a
severe psychological toll on the characters - 2B succumbs to the Logic Virus but not before confessing her love for 9S in an audio log, and 9S himself essentially goes insane with grief and rage.
But yeah, for the first two routes you aren't given much context or details on what's going on other than "go kill the evil machines to reclaim the Earth for humanity." It's certainly a poor way to hold your audience's attention if they don't know your MO though.
As for the story in
XIV itself, it does appear to be relying on familiarity with the characters and story of
Automata to keep your interest... which is a problem.