The Emperor's first obstacle to the reunification of Mankind was the existence of the Mechanicumempire of the Tech-priests of the Cult Mechanicuson Mars, who had historically been fiercely independent of Earth. Instead of an outright war, the Emperor used the threat of an assault by his Space Marines on Mars and the offer of new technologies to form an alliance in the 30th Millennium with the Tech-priests of what would later be called the Adeptus Mechanicus. This alliance formed the heart of the newborn Imperium of Man and was symbolised by the adoption of the two headed-eagle or Aquila that is still the primary icon of the Imperium.
Despite his disdain for their reliance on religion and cybernetic augmentation of their bodies, the Emperor knew that He would need Mars' great manufactoria (factories), mechanical output and ancient technological knowledge to build the military force required to reunify humanity across the galaxy, and He incorporated them into the Imperium.
The Tech-priests of Mars, likewise, saw the Emperor's extraordinary scientific knowledge and technological skill as proof that He was the Omnissiah, the living avatar of their Machine God in the material realm, who the creed of the Cult Mechanicus had promised would return one day to the Red Planet and offer the true way forward for humanity.