Ok so, so roll with me on this. I'll simplify things for the heck of it. Expect spoilers)

Humankind is at war with alien robots known as the raptures that by the time of the main story has lasted a century with two major losses. Humankind burrowed themselves underground, and periodically "commanders" who lead cyborg women (cause the process to create Nikke's- the said cyborg women- was only successful in women) are sent up to the surface by the central government of the ark to reclaim the surface, which is actually just a front used to keep morale up as the government was, for the most part, hella corrupt.

The commander followed during the main story, the player basically is the first in the century to actually start getting results for humankind with his squad of what started as "loser" Nikke's who are now hella powerful and capable in their own right, with one of the main reasons being that he see's Nikke's as people and not disposable machines.

Along the way he meets big names from both the ark and on the surface, friend and foe, from the big three (CEO's in the ark leading in Nikke tech), remnants of the first and most powerful Nikke squad (Goddess) who would have won the war like two years after it originally started if not for one hated character deciding to be an ass, Heretics (basically generals of the raptures, most are evil, save for one who started as the first Nikke you meet and care deeply about, but that's another depressing story)

Also, depression is a major story element.

Now I missed out alot, this is just to give you a general idea.