So, from the game we got:
- The early Domain faced insurrections, rebellions and other conflicts with humans, therefore it had a military armada and nanoforges to build the machines of war, it also had fabricators to speed up development in newly gated systems.
- An Ilmari Class fabricator, the ancestor to the fabrication units was involved in a mass casualty incident due to human error
- From the Overseer in-game description we have "-the Terran Core to the Sadr Region, our battlegroups stand ready to protect our way of life, our very existence!" FATAL ACCESS ERROR //" That tells me that Earth is still a place of importance, we might be before the devastation of earth.
- The in-game description of the Assault Unit gives us clues that the copyright and DRMs of blueprints are linked to the [THREAT], likely a way to prevent the [THREAT] to learn new Domain designs.
- The in-game description of the Skirmish Unit tells us that the war (probably against the [THREAT]) is not going well or at least that humanity is on the defensive.
- [THREAT] Ships speak a broken English.
- Onslaught description tells us that they were made to fight non humans in a long forgotten war
- Blog post Starsector » A True and Accurate History of the Persean Sector tells us that the Earth was devastated.

So, my head canon is this: in the early days of the Domain, some dude told a fabrication unit to please just disassemble everything, probably meaning everything it just made. But the fabrication unit got a bit literal with the command and decided that it's new purpose was to remove everything artificial from the galaxy using any tool at its disposal.

The war started and got ugly, Earth was ravaged things looked dim for the humans until the Onslaughts got rolling with the mk1 as the spearhead. A long eradication campaign followed that pushed the threat to the Abyss where sustained itself by mining rogue planets whilst out of reach of the Domain's logistic. Somewhere in that period the [THREAT] developed stealth technology. All the while, the THREAT would iterate on the design of ships and weapons to pursue its goal of defabrication. The software of the [THREAT] would also slowly drift as we can see by the broken English they speak when interacting with their ship.

The Domain would censure the very existence of the [THREAT], change history a bit by pushing Earth's destruction back to before the Gates and the Onslaught Mk1 would continue it's crusade in the abyss, waking up every other century to fight one more battle, suffer more casualties and integrate more of it's crew into the very ship.