Omnissiah

In Warhammer 40,000, things are so grimdark that people have forgotten all of the science that was once known; the only remaining knowledge is encoded in religious ceremonies followed by the Adeptus Mechanicus. The deity central to mechanicus dogma is the Machine God, who is also known as the Omnissiah. While this may seem straight forward, the actual identity of Omnissiah has become the greatest game of 'Guess Who?' in 40k, as several theories of his true form have now come forward, which are covered below.

Theory One: God-Emperor of Mankind

Some tech-priests believe that the God-Emperor of Mankind is the Omnissiah, or at least a form of him. These include the tech-priests who remained loyal to the Imperium of Man during the Horus Heresy. The Adeptus Mechanicus officially holds this view, and it is used to pacify the more zealous member of the Ecclesiarchy and Inquisition who doubt the Mechanicum's loyalty, though there are many individuals who believe they are separate. This logically though does lead to causes of conflict between the two bodies and it is something that will never truly be satisfied by either side.

Theory Two: Void Dragon

Other tech-priests equate the Omnissiah with the Void Dragon, one of the Star Gods of the Necrons. These tech-priests also tend to venerate the Necrons as the Omnissiah's angels. They then tend to do stupid things like poking around in Necron tombs, trying to probe them for secrets as part of their "Quest For Knowledge." They tend not to live very long, as Necrons don't care what any life-forms think of them; they are equal-opportunity destroyers. In the recent Horus Heresy fluff, it was shown the Emperor sealed a silver dragon under Mars in the distant past in order so humanity could have control over machines. Somehow he was able to make it so humans could take some of the dragon's power then for their own although in hindsight putting a super powerful creature in the same solar system as the capital of the Imperium might come back to bite them in the ass...

Theory three: Both

Some versions of the myth tend to separate them in two, with the Void Dragon being the Machine God, and the Emperor being the Omnissiah who "tamed" him. It's unclear, really

Theory four: Chaos Undivided

The Dark Mechanicus, those tech-priests who sided with the Chaos Space Marines during the Horus Heresy, believe that the Omnissiah is a combined aspect of Chaos Undivided, worshiping Chaos as a form of progress and knowledge. Said tech-priests tend to take the mechanical augmentations a little further than one would like in a tech-priest. They also use bio-mechanics, which is very explicitly forbidden.

Theory five: Individual warp entity

It could be over time that like any other strong collective desire and belief the tech-priests have created their own God in the warp, which would be a Machine God of logic, machines and arcane processes. While he may have started off as one of the other theories, such belief just doesn't do anything and proof of previous miracles caused by strong belief in the god and his servants the machine spirits have been seen.

Other

Presumably, any sufficiently-advanced machine will be taken for the Machine God by at least some tech-priests, like a functional Man of Iron, or other Dark Age technology. They could for example worship a rediscovered ipod as a significant avatar of his machineness.