As the Imperium grew and the Great Crusade fractured into hundreds of different Expeditionary Fleets that could be separate from one another for solar decades of relative time, the Primarchs and their Emperor began to grow distant from each other. The Night Lords and World Eaters Legionsgrew infamous for their ever-greater atrocities during the conquest of new worlds, the Thousand Sons' pursuit of knowledge transformed into the use of sorcery through the temptations secretly offered by Tzeentch, and the Word Bearers' fanatical religious beliefs in the Emperor's divinity led to a rift between them and the Emperor when He dramatically rejected their attempts at worship in light of the atheistic nature of the Imperial Truthhe sought to impress on all the worlds of the Imperium.
The Imperial Army, composed almost entirely of normal human soldiers (some regiments such as the Geno Two-Five Chilliad were the products of selective breeding and genetic-engineering dating back to the Unification Wars to produce more capable soldiers or officers), provided much-needed manpower for garrison and support duties for the planets brought into Imperial Compliance by the Crusade.
Freed from garrison duties, the Space Marines who comprised the core of each Expeditionary Fleet could conquer yet more worlds in a shorter space of time. Many Astartes and Imperial Army soldiers began speaking only of their loyalty to the Primarch that they served, and not to their Emperor. Owing to the isolation between the Legions and the Emperor after the Ullanor Crusadewhen the Emperor returned to Terra and left the Great Crusade in the hands of His favoured son Horus as the new Imperial Warmaster, this growing breach between the military and the people of the Imperium as represented by the Emperor essentially went unnoticed back on Terra.