Though as the Emperor was busy preparing for the Primarchs and their legions to set out into the stars, the Chaos gods saw perhaps opportunity, or the dangers of what the Emperor had planned. Every chapter had one Primarch and the 'gene-seed' based on the Primarch's own, unique genetic code. Shortly after, he set his sights on the stars and with the help of the Adeptus Mechanicus (A cult following a presumed machine-god, situated on Mars) was able to create the vessels to start what became known as the Great Crusade, aiming to unify all of humanity.During this time the Emperor had created the Primarchs, sown from his very own genes. Throughout these unification wars, he was able to create the first genetically engineered super soldiers and was able to unify all that opposed him. His beginning was that of a warlord among many who sought to rule all of Terra, and in the end he was the sole victor. The most ancient records only go back as far as pre-unification of Terra (Humanity's home world, aka Earth). As the millenniums passed however, betrayal and horror would befall him. As his powers grew, so was his ability to unify those around him.

Then as the years went on he decided to take a more direct approach to helping humanity. In that time, he mostly watched as humanity gave into the temptations and beliefs of the chaos gods. He was the first of many psykers or shamans as they were known back then. Not much is known about the Emperor before he unified Terra and the rest of humanity, except that he was an ancient man, who lived many lives. Even though his body can no longer sustain life, his mind carries on with the sacrifices of 1000 Psykers a day and the sheer vigilance to stop chaos from destroying the Imperium of Man.

As of the current lore of Warhammer 40,000, the Emperor of Man is shattered husk of a man on the Golden Throne.

Emperor of mankind vs horus