It must be the Void Dragon. But didn't the Emperor think, what would happen if the Void Dragon broke free.
Maybe the Emperor is just a dunce and does't realize it is the Void Dragon But more seriously I'll have to go with some sort of A.I. Think about it: the robots rebel, then humanity begins a grand purge of them. The smarter machines decide to masquerade as some arcano-tech-witch fantasy to preserve their existence. Perhaps the Omnissiah is the smartest of these machines, or some collective of A.I.'s, represented by the machine spirits all over the Imperium.
The Omnissiah is actually McGyver, seated in an additional Golden Throne he made back in the 1990 when he found himself with a a bit of rubber wire, some chewing gum and plenty of sparetime. To be serious, I think it's the Void Dragon, albeit the new Necron Codex drastically changed the relation between Necrons and C'tan.
The Emperor imprisoned the void dragon on mars and is leeching his power to empower technology with "spirits" which is how youre humble lasgun has a spirit that you can anger with delayed maintenance
It's a very strange case. It is more than likely that it is the Void Dragon; however the Emperor did not imprison the VD, he merely "closed the door" to its conscience so that servants of Mars couldn't get to it. I believe in the Horus Heresy novel Mechanicum, the Fabricator General says as soon as their alliance was made, the Emperor walked straight to the deep dark parts of Mars and sealed the door to all. At least I believe that was the VD's room, and not some other evil entity. But then the question is, since none of the other Tech Magi knew of the room's existence, how did they gleam knowledge from it. And then when the door is unlocked, that is when the rebellion begins and the Dark Mechanicus is formed as mechanicus/warp-spawn hybrid. So the question, who can truly say?
some reading materials, spoilers for the book "Mechanicum" http://wh40k.lexicanum.com/wiki/Dragon_of_Mars#.UsB_bPQW2Bo
The emperor lives through the spirit of the machines, his essence encoded into the very materials of their construction. The golden throne of the emperor facilitates this in much the same way as an open conduit to the universe allowing his presence to shine through with his holy presence.
Machine spirits aren't even true AI's, just a collection of programs. They get corrupted over time, some routines getting degraded while others get adjusted as a new generation of techpriests repair the machine and 'tweak' things as the understanding of these devices continues to degrade. This can lead to them coming across as having some kind of 'personality' of their own, but really their programming has just changed from original factory settings. It's more obvious in the bigger vehicles as the programming in their core is much more complex. The only difference between a machine spirit and a cogitator is that a cogitator functions from manual input, while a machine spirit takes information from its surroundings and operates in line with its programming. It's basically a good computer. As for the Omnissiah itself? Well... in my opinion it's either a figment of the machine cults imagination that's a carry over from the reliance on tech in the dark age of technology and the increasing amount of ritualisation in maintenance as more and more understanding of how stuff works is lost or... they worship the void dragon unknowingly.
More than likely it is the Void Dragon, slowly yet surely corrupting the Mechanicum, twisting the Priesthood of Mars from within. That and the goals/motivations of the C'Tan are rather inscrutable and arcane. Mayhap it has a goal that is simply beyond the ken of mortal understanding.
