So, major spoilers for the Copied Factory ahoy!
Bosses are a powerful variant of a machine, a new machine named Hobbes (in the grand tradition of naming key machines after famous philosophers), the famous Goliath-class Engels, and 9S in a flight unit hijacking a quadrupedal machine tank for extra firepower.
Nothing is really explained as to what's going on - you get into (or are forced into) the excavation tunnel, save 2P along with the dwarven twins, and then go down into the Copied Factory to quell the threat 2P says the machines present. 2P and 9S end up being put out of commission at the end, and not much else happens.
However, more things happen afterwards...
After clearing the instance, you're given free reign to explore an instanced version of the Copied Factory with the dwarven twins seeking some sort of "key" mentioned by 2P before she went offline. You find a bunch of junk they believe will suffice, along with a damaged pod that is going to take six months to analyze said junk.
While exploring, you also find a number of data logs:
Unidentified Expedition Log [1/2/3]
-Survey of local terrain continues. Ecosystem in this area appears to have adapted to extended drought - dry climate conditions must have been present for some time. Investigation of a murky spring did reveal aquatic life, though of an unusual sort. / Survey of local terrain continues. Current location is particularly verdant, likely owing to the plethora of freshwater springs. Peculiar that two so markedly distinct biomes should exist in such proximity. / Survey of local terrain still continues, though with no discoveries of particular note, Or perhaps I've grown tired of searching. Still, it's better to be stuck in the middle of nowhere than on the front lines.
Memory of a Damaged Machine
-Oh brother, where art thou? It's dark. I'm alone. All alone and lonely. I want friends. Don't stop me. I'll kill you. I need friends...
Machine Research Report [1/2]
-The machines' primary objective seems to be nothing more than "kill enemy." What's troubling, though, is that their auto-evolution systems have begun to build a private network. / The machines' network has evolved o the point where paradoxes no longer present an obstacle, allowing for diversity among individuals. They may continue to incorporate whatever data is within reach - someday, the world in its entirety.
Weapon Fragment Data [1/2/3/4]
-The blade is in motion, once-gleaming white drenched red. A blow to halt the twin gears life and death, its impetus long forgotten. / Our world never doubted. Only closed its eyes, the better to turn unburdened. / In that world we once knew, sharp and shattered, a single spark of memory grows to a flame. It shines upon the lost, and at last we understand. / Rue not what has come to be, nor lay down your arms while life still rises amidst ruin. The blade demands this vow, this virtue.
Tattered Flyer
-Thanks for [...] by! [...]'s is a thriving chain of [... ...]cluding swords that match the regional features and squads of [...]
If I missed any logs, someone please let me know.
There is also an extra room that can only be entered during the instanced exploration; during the duty the doors in are shut. Said room is full of nonfunctional (likely dead) copies of 2B.
Before setting out on your exploration, you're forced to choose between going with Konogg (the male dwarf in black) or Anogg (the female dwarf in white); the former does not trust 2P, while the latter does. Other than your companion for that quest and a little bit of writing in the journal, there is no discernible difference in outcomes at the moment.
Observation:
While everything seems fine at the outset, once you reach the climax and ending areas, the factory seems to be falling apart as if from Primordial Light contamination or the humanity-dooming White Chlorination Syndrome from the original NieR.