Machine God

The Machine God (also known as the Omnissiah or Deus Mechanicus) is the theological entity worshipped by the Adepts of the Adeptus Mechanicus as the bestower of all technology and scientific wisdom. For many in the Imperium of Man, this belief conflicts with the orthodox theology of the Imperial Cult where the only God of humanity is the Emperor of Mankind. But since the Adeptus Mechanicus is vital to the survival of the Imperium, conflict over this issue is often avoided by the Mechanicus' willing conflation of the Machine God's avatar in the physical world, the Omnissiah, with the Emperor himself. This compromise truly satisfies neither believers in the Cult Mechanicus or the Imperial Cult, but it keeps the piece between the two religions and the Imperium functioning.

Aspects of Worship
According to the teachings of the Adeptus Mechanicus' Cult Mechanicus, knowledge is the supreme manifestation of divinity, and all creatures and artifacts that embody knowledge are holy because of it. Machines that preserve knowledge from ancient times are also holy, and machine intelligences are no less divine than those of flesh and blood. A man's worth is only the sum of his knowledge - his body is simply an organic machine capable of preserving intellect.

Alternative Theories
The Machine God may actually be the C'tan Void Dragon, an ancient entity of immense power. It is imprisoned in a stasis tomb on Mars. The mighty C´tan was imprisoned by the God-emperor himself. The God-Emperor in the far past was unable to kill the C´tan, he imprisoned him on Mars so the powers of the C´tan, though passive, would cause the Adeptus Mechanicus to emerge, which the Emperor needed as support for his Grand Crusade. This so called "Grand lie of Mars" is buried deep beneath the sands of Mars in a Cave which is actually the Dragon itself. when the Cave was visited by a few agents of Adept Zeth it turned out the Dragon was both entity and space.

This truth has been more convincing since the mass awakening of the Necron army. It is said that a small amount of Necron forces managed to breach Imperial defences in the Segmentum Solar and perform a landing on Mars itself after destroying some of the Noctis Labyrinth Mine Complexes.

Upon landing, countless Mechanicus forces quickly dispatched the Necron expedition. Although the Necrons were eliminated, their purpose on Mars is unknown. More striking is the fact that they breached vast areas of Imperial space (including the Segmentum Solar itself) undetected. The Mechanicus enforced a perdita zone around the entire Noctis Labyrinth, enforced by an entire Skitarii Legion.