From Lexicanum

The Early Crusade

The Great Crusade was a brief age of rebuilding and reunification following the complete regression of mankind during the Age of Strife. It was a time when the Emperor still lived in the conventional sense, and led his race in person.

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.

At the end of the warp storms which had plagued the galaxy, the Emperor was able to begin the Great Crusade that would create the Imperium. 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.

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 Great Crusade spread into M31. The Legions had been battling constantly, especially the Iron Warriors, fighting the monotony of siege warfare and garrison duties. Also, the Primarchs had begun to separate. Certain Primarchs hated each other, Perturabo was shunned by most and was in turn envious of Rogal Dorn, while Dorn himself harbored a mutual dislike of Roboute Guilliman that continued into the creation of the Codex Astartes. These mistrusts and hatreds would form the linchpin of the Horus Heresy.

The End of the Crusade

The Great Crusade continued until the virus bombing of Isstvan III. From this point on, Horus was the enemy and the Great Crusade was over. The loyalist legions were recalled to Terra to defend against the Warmaster, but the Ultramarines remained in the outer fringes. This is why most of the later Chapter foundings were primarily from the Ultramarines; they didn't suffer the high casualties the other legions incurred at the defense of the Imperial Palace.

With the Emperor's near-death and the cancer of heresy taking root even among the Legiones Astartes, the Imperium began to degenerate into the state it is now, with fear and chaos rife, Inquisitors seeking out heresy at every corner and millions of people living in forced, and willing, slavery to their God-Emperor.