The Early Crusade
Part of the Emperor's vision of human unification was the Primarch Project, meant to be the creation of 20 superhumans to lead the Emperor's forces to reclaim the galaxy in his name. It also saw the creation of the Space Marine Legions from the gene-seed samples that survived the scattering of the Primarchs by the Chaos gods. These forces would play the major role in the Great Crusade.
The subsiding of the warp storms plaguing much of the galaxy coincided with the end of the Age of Strife. With warp travel feasible again, the Emperor was able to begin the Great Crusade which would create the Imperium.
Even before the warp storms and the Age of Strife had ended, the Emperor had begun to make plans for the Great Crusade. These plans included the creation of a far more advanced form of power armour required for the conditions of deep space and alien worlds.
After securing Luna and then Mars, he began a great building project, reconstructing the industries and production facilities he would need to construct and maintain a great space fleet, sufficient to carry his legions all the way to the edges of the galaxy. Mars, due to its advanced technology and manufacturing infrastructure, became the center of this development, producing, along with ships, the arms and armor his warriors would be equipped with.
The Crusade begins
His fleet constructed, he forged out into the depths of space, seeking out his Primarchs and spreading the name of the Emperor. Throughout the following millennium, he gradually reclaimed his Primarchs, and slowly united humanity under the Pax Imperialis.
As each Primarch was discovered, he was given control of his own Legion of Space Marines. As more of the Empire was carved, the Emperor's forces were spread more and more thinly. Eventually the need for Space Marines was greater than the supply. As such, Accelerated Gene Culturing was necessary to provide sufficient legions. Unfortunately, this process was unstable and led to flaws in the gene seed of the legions. This would lead to such afflictions as the Black Rage and various mutations in the Space Wolf gene seed.
The Crusade lasted for around two hundred years. Towards its end came a period of political consolidation. The Legions were at this point dispersed across the galaxy, many acting as garrison forces rather than campaigning armies. The Legions had been battling constantly, especially the Iron Warriors, struggling under the monotony of siege warfare and garrison duties. Also, the Primarchs that had previously friendly rivalries were beginning to develop into dangerous feuds. Some of the Primarchs had reached the point of intolerance with one another, others like Magnus the Red had simply become isolated in the confusion of the Great Crusade. Perturabo was shunned by most due to the nature of his hand in the Crusade and was in turn envious of Rogal Dorn. Konrad Curze also had a disagreement with Dorn that escalated into a brutal surprise attack that left Dorn badly injured and unconscious. This mistrust and hatred would form the linchpin of the Horus Heresy.
The End of the Crusade
The age of the Great Crusade ended with the virus bombing of Isstvan III. The loyalist legions were recalled to Terra to defend against the traitor Warmaster Horus, but not all of the Legions were able to return. The Ultramarines were mired in the Ultramar system fighting Kor Phaeron and his retinue of Word Bearers that had come to destroy them. The Space Wolves were finishing their battle at Prospero with the now openly traitorous Thousand Sons and the Dark Angels were in the midst of a civil war on Caliban.
In many ways the Emperor was now gone, The Imperium suddenly finding itself without the great leadership of the Guardian of Mankind. The brief age of recovery which the Great Crusade represented was over, and mankind began to decline into the state it is now, with fear and chaos rife, Inquisitors seeking out heresy at every corner and billions of people living in forced, and willing, slavery to their God-Emperor.