After the destruction of the last church on earth he committed the biggest blot on his history and destroyed his thunder worriers because they were a means to an end and wouldn’t fit into a time of piece being brutish barbarians in a time of war, while some survived they weren’t the more refined worriers that the space marines are and didn’t have the extremely long life spans and so they died off.
Having done this the Emperor decided to create 20 god-like beings of immense power from his own blood to be his sons who were known as the primearchs. It is not known exactly how or why the Primearchs were made but there is much speculation on this but there was also the matter of the gods of chaos who were the embodiment of all sorts of evil.The Emperors main ghoul is to destroy them and so to prevent this they used there demonic power’s to take the primearchs and send them through the warp wile in there infancy causing each of them to fall on different planets, when the Emperor discovered this he decided to create 20 legions of space marines from the primearchs genes and took them and his personal bodyguard the adeptus custodies and set out on the great crusade saving, retaking or annihilating any human planets they found and gradually reclaiming the primearchs along the way.
Once all the primearchs were all found the Emperor eventually decided to leave the great crusade to return to Earth now called Terra and begin working on a project being the creation of a human webway to provide safer, more stable and faster travel removing human dependence on using the warp to travel but due to the importance of this he didn’t even tell his sons especially his favoured son Horus who he had now left in charge of the crusade with the title of Warmaster.
The Horus Herasy:
The Horus Heresy Began During the final days of the Great Crusade when the primearch Horus was struck by a daemon blade of Nurgle known as the Anathema which infected him in a trap set by lorgar by corrupting Lugin Tembar a friend of Horus. Horus’s Captains didn’t know how to heal him and so took him to a planet were unknown chaos worshippers healed him and Lorgar in conspiracy with the tainted chaplin Erabus who both had already turned.
Lorgar was in disguise there to give him a vision of the future in total chaos as a result of the emperor’s rule. During the vision however the primearch Magnus appeared in his vision as a wolf to try and save him but was to late, later causing the burning of Prospero and Magnus joining Horus and chaos.
Horus having know fallen to Chaos his first out-rite act againsed the imperium was on istvan 3 sending down all known loyalist cells in his corrupted legion and then virus bombing the planet killing billions of inhabitants and his forces with a psychic backlash blacking out the light of the astra-nomican in the warp for a short period of time. Horus then waited on istvan 5 to wait for the imperiums retaliation, 7 legions were cent to the planet to bring Horus back to Terra for trial. However 4 of these legions cent were already loyal to chaos and Horus.
As the forces landed a massacre began with all the traitor legions surrounding the 3 loyal ones being the Raven Guard, The Salamanders and the Iron Hands with the loyal legions gaining massive casualty counts and the death of Ferrus Manus the primearch of the Iron Hands who was Decapitated by his once closest brother Fulgrim of the Emperor’s Children.