Nightmare Engine

The Deus Ex Machina was supposed to be crowning achievement of the techmaturgic might of the Second Empire. The godlike artificial intellect that the empire willingly gestalted in the Network, the pseudodimension used by it as a much more alien equivalent of the internet, to govern and oversee all of the Network's data vaults, and all of the techmaturgic items that were to a various degree connected to the Network.
In the Empire's defense, they spend almost a century in learning all they could about the entity they were planning to create and about the way they operated. They were hundreds of contingency plans and failsafes in place. What's more, the Deus Ex Machina worked wonderfully well for more than two centuries, bringing the imperial civilization to its peak. What's more, the imperials truly couldn't foresee that the entire cosmology is going to bluescreen on them, and the high gods that simply didn't exist yesterday were going to corrupt the Deus Ex Machina out of the blue.
The contingency plans and failsafes saved the Grand Empire, in the end. The only reason why the Deus Ex Machina (soon renamed into Hexmachina by the survivors) failed to finish the war in the first twenty minutes was because the metaphysical shutters in the Network has severed the connection between the civilian and military subnetworks, trapping the Hexmachina in the former. This meant that while the world around them was ending (the death toll of initial Hexmachina attack is estimate to reach upward of eight hundred million during the first twenty four hours), the scattered units of the Imperial Army maintained control over their equipment and could communicate to coordinate their desperate counterattacks.
What was supposed to be a swift take-over turned into a total war. Even with the help of the first Chosen Ones and theurgists, the Empire was barely holding to whatever was left from it after the initial attack. When the Hexmachina finally breached the techmaturgic walls of the military network, the Imperial Army 'teleported' whatever Chosen Ones and soldiers they had on hand to the Network (a road without return), and had them fight the Hexmachina - and somehow, they succeded in slaying it. Or at least the overwhelming majority of the Hexmachina that was poured into the military network. This ended the Twilight War - but started the Nightmare Engine.

Structure

It is unknown if there is an 'organization structure' to speak off among the ranks of the Nightmare Engine. The vestiges of the Hexmachina that are in charge of it simply lack the processing power to coordinate any larger activity from its remaining assets - while its ranks are technically endless, the Hexmachina is only capable of marshalling a minuscule fraction of them at any given moment. As a result, the entire faction is practically composed of only its leader and a small number of technically equal (and equally expendable) 'soldiers' that the leader is controlling directly.
This includes the few of its domains in the Lost Lands. In fact, it is speculated that simultaneous assault on all of them at once would simply overwhelm the Hexmachina to the point where it could only operate a fraction of the defenders at once (or would have to abandon most of them), not to mention temporarily halting all other operations. However coordinating such an operation in the deepest recesses of the Lost Lands is beyond any other faction (or even an alliance of factions)'s ability.

Military

Hunter/Killer Spirits are the main force of the Nightmare Engine. They used to be create so erase dangerous data and illegal network spirits, but when the Twilight War started, they were quickly upgraded by the Hexmachina to fit different purpose. Today they are populating whatever remains of the Network. When a mortal techmaturgists attempts to gain access to whatever they are guarding (or uses a techmaturgic item that happens to use Network and the connection happens to go somewhere in the relatively closeness of the H/KS lair), they immediately attack.
They are capable of crossing into Reality, and will possess the nearest techmaturgic item (if it's installed into the techmaturgist's body or he is keeping it in their hands, the results are... bad) and will, if possible, attempt to use it to kill anyone in the vicinity. By either using its functions incorectly or by having it self-destruct violently. If not eliminated fast enough, the H/KS grasp on the Reality will improve to the point where it becomes capable of altering it.
This typically means drawing all nearby techmaturgic objects or raw materials in and warping itself an indefatigable body of steel and crystal, that it then uses to continue the slaughter. All of the few domains of the Engine in the Lost Lands are places where such an event thoroughly overwhelmed whoever triggered it, resulting in more H/KS crossing into Reality and warping themselves not only bodies, but also an entire fortified base.