The Emperor and the Heresy
"It is better to die for the Emperor, than die for yourself."

The Immortal God Emperor of Mankind is the leader of the Imperium, the largest human organisation of the time.
Early history
According to canon works by White Dwarf, humanity originally was aware of the Warp and coexisted with it. There were certain gifted individuals who could communicate with the Warp and use it for many purposes - the tribal healers, shamans, medicine men and other spiritual leaders of early humanity. These people's spirits could even flow through the Warp seamlessly after death and be reborn in new human bodies.
However, as humanity gained more knowledge, their secret desires for more power and pleasures grew and corruption began. The spiritual leaders began to notice the changes as their psychic gifts diminished and reincarnation became harder. They called a great council, in which the leaders decided none of them alone could stop this deterioration - but perhaps together they could. They decided that they would take their own lives in order to be reborn as a god of unimaginable power.
Almost a year after this council and the resulting suicides, a child was born - the boy who would become the Immortal God Emperor of all Mankind. His original name is unknown, although there are some references in Warhammer 40,000 canon that he was born in the 8th millennium in central Anatolia (Priestley and Ansell, 1990; Abnett, 2006). He grew up in an isolated and poor rural area and it was rumoured that he had the power to stop his own aging and numerous other potent and miraculous psychic abilities.
After many years, as the Emperor grew in wisdom and focus, he intuitively knew of the spiritual corruption caused by human behaviour and set out to correct it. He always remained in the background, facilitating some of humanity’s most important changes and generally guiding and protecting the species. He bore many different names in many different eras of human history, sometimes taking on the identity of men who became great historical personages who directed humanity along a positive track. Other times, he simply took anonymous identities, prodding and pushing humanity along a path that would lead to the greatest enlightenment and happiness for all where and whenever he could.
The first mention of the Emperor in Imperial records is when he unified Terra after the Age of Strife (sometime in the 29th Millennium). The Emperor's use of genetically engineered warriors--the protoastartes, genowarriors, pre-Space Marines-- enabled him to reunite the people of Earth and to set his sights on the stars. With the assistance of the Adeptus Mechanicus on Mars, the Emperor armed his Space Marines and fleets of interstellar ships to carry his armies to the farthest reaches of the galaxy and spread the Imperium of Mankind.
The Emperor also created the superhuman Primarchs from his own genetic template from whom the Space Marines' geneseed was later developed, but an event of unknown cause, most likely the intervention of the Chaos Gods, scattered the Primarchs across human-inhabited worlds in the galaxy from the laboratory beneath the Himalaya Mountains where the Emperor had created them.
The Great Crusade
The Emperor had a grand vision: to reunite the elements of humanity who had been scattered across the galaxy and isolated from each other during the Age of Strife. In the initial years of the Great Crusade, the Emperor was at the forefront of the fighting, leading his genetically-engineered soldiers into battle. As more worlds came under the control of the fledgling Imperium of Mankind, the Emperor rediscovered the lost Primarchs, whose genetic template was used to stabilise the creation process of the Space Marines.
Following the Triumph at Ullanor the Emperor returned to his underground laboratories on Terra to work on secret projects, including the mapping of the Webway, an entrance to which he had discovered within his mountain fastness. He left his trusted 'sons', the Primarchs, in control of the Crusade, promoting the foremost of these, Horus, to the rank of Warmaster of the Imperium. Crucially he did not explain to anyone, including Horus, what he was planning to do or why he had returned to Terra, sowing the first seeds of discontent.

The Horus Heresy
The Great Crusade came to an end with the events of the Horus Heresy, when Horus turned on the Emperor. Under Horus's leadership, nine Space Marine Legions and many Imperial Army regiments turned to Chaos and started a galactic civil war.
Even as Horus's armies laid siege to Terra, the Emperor still believed that Horus could be redeemed, and he maintained this belief even as he faced Horus in single combat. Due to The Emperor's unwillingness to use his full power against the man who had once been his closest son, he suffered grievous injuries at Horus's hands. As Horus stood over the Emperor's shattered body, an Adeptus Custode entered the room. Horus flayed him alive with a single look. The Adeptus Custode's death galvanised the Emperor. He saw with sudden clarity how far fallen Horus had gone into the arms of Chaos, that was there only way to break their hold on him: to kill his beloved son. The Emperor mustered a psychic attack of unparalleled power and unleashed it on Horus. So powerful was the attack that the Chaos Gods withdrew their power from Horus's body, terrified that the Emperor would kill them if they stayed; and for a split second, the Emperor sensed the return of his son's sanity. Yet the Emperor also knew he could not let Horus live, for he would not be there to stop the Chaos gods should they attempt to move their pawn again. Driving all compassion from his mind, the Emperor directed another yet more powerful psychic attack obliterating Horus from the mortal plane, obliterating his very soul.
Present day
The Emperor's broken body was discovered by Rogal Dorn who, following the Emperor's instructions, oversaw the Emperor's re-connection to the Golden Throne, an arcane device of technomagic, to sustain his spirit. The Emperor has remained in the Golden Throne since his 'ascension' to this day, neither fully living nor dead. Although initially designed as the hub of the Emperor's project to colonise the webway, the Golden Throne also functions as a complex life support device. The Golden Throne itself lies in the Sanctum Imperialis, which is guarded by the Emperor's Custodian Guard, also known as the Adeptus Custodes. The Emperor's physical form is preserved and his life functions are carried out by carefully maintained machinery.
The Golden Throne is also connected to a massive Warp beacon known as the Astronomican that generates the system of signals making faster than light travel in the Imperium possible by providing a beacon with which astropaths are able to navigate. The Emperor himself focuses this signal, also known as the Ray of Hope or the Golden Path, but much of the power behind it is supplied by a "chorus" of ten thousand human psykers. The life force of the psykers is consumed within several months (Priestley, 1998), which forces replacements being constantly brought to Terra on the infamous Black Ships of the Inquisition.
Religious aspects
The Emperor, commonly known as "The God-Emperor of Mankind", is worshipped as an omni-present deity by most Imperial citizens. Belief and worship is taught and upheld by the Imperium, and disobedience is universally punished by death. Imperial citizens believe the Emperor guides and watches over them, protecting them from the horrors of the Immaterium. There are doubters, and some rumours circulate that the Emperor is long-dead, and the Golden Throne is nothing but an empty shell of machinery to fool the countless billions. These are instantly dismissed as heresy by the Inquisition and such doubters would be summarily executed, and are incorrect: the Imperium's astropaths need to be bound to the Emperor's spirit in order to have the power to communicate across interstellar space, so if they still exist, then so does the Emperor.
The opening story text of the Inquisitor rulebook describes the mixed feelings that surrounded the Emperor's ascension. The Emperor had ordered Rogal Dorn and his retainers to reconnect him to the Golden Throne. While he he would never walk among his subjects again, his psychic powers would return in time; and the Astronomican would endure, and the webway tunnel would remain closed. Many voiced concerns over the Emperor's self-imposed duty, for without the Imperium's creator to lead humanity in person, they argued, what hope did the Imperium have for survival?
Had it been possible for the Emperor to return, members of the newly-formed Inquisition and the High Lords of Terra would have opposed it. They feared such an event, so soon after the Horus Heresy, could destroy the Imperium. They also are feared changes to the Emperor resulting from his ascension.
Some within the Imperium believe the Emperor must be allowed to die fully in order to be reborn as a new power in the warp, the so-called 'Star Child' and if this happened, not one of the Imperium's enemies would be safe from his wrath. Rumors abound that the Emperor walks among his people; on countless worlds he is worshipped as a God. It is highly possible that the Emperor is truly in two places at once, as the man who once was the Warrior-Lord of the Human race, and yet still seated as the Half-Dead God of the Imperium.
Alternate history
The Realm of Chaos books described a couple of extra aspects of the Emperor. Firstly that during his lifetime he fathered a number of children who gained some of his powers of immortality but were also psychically shielded from him. These "Sensei" are a force for good but kept themselves hidden. The second is that the Emperor's spirit is trapped by the golden throne and he is in effect in a state of limbo. If the throne was destroyed he would be reborn as the "Star Child" and be whole again and able to protect humanity properly once more. These aspects are not referenced on the current canon, so it is unknown if they are still part of it.
