What is known of the immortal being before he came to the Emperor is very little, his origin and history prior to unifying Terra is left largely mysterious and undetailed, though certain sources indicate he was born around the 8,000 BC in Central Anatolia (today Turkey) as the reincarnation of a thousand shaman souls who ritualistically sacrificed themselves to merge together and create the perfect being who would stand against the rising forces of the Warp. As he grew older, his potent psychic powers began to manifest - his psychic power was so great that its energies altered his genome and physiology in the womb and rendered him immortal and so, he watched humanity's development over the course of human history, at times guiding it from the shadows, at other moments taking a more active role and serving as a prophet, general or sage as needed. Its hinted that among many of these aliases included Jesus Christ, Buddha, Jehova, Brahma, Allah and several other divine figures.
The Rise of the Imperium
The official first appearance of the Emperor was during the Age of Strife in the 30th Millennium, a chaotic period that saw mankind dispersed and broken. He was just one of the many warlords struggling for control in war-torn Earth. He was aware that the darker extremes of human nature were feeding the growth of the Chaos Gods in the Warp, and so he sought to promote peace and harmony on Earth and thereby curb the growth of the Ruinous Powers' strength. He finally emerged from the shadows to take a more direct hand in guiding mankind, conquering the warring nations on the Planet Terra and establishing his rule over them.
With Earth finally brought to heel, he turned his gaze to the rest of the galaxy. Prior to the Dark Age of Technology, mankind managed to spread their presence across the stars and colonizing thousands of systems and planets with the use of the Warp for space travel by human beings, with the greatest extent of interstellar space exploration and colonization across the galaxy taking place during this period after the development of the Warp-Drive that allowed faster-than-light space travel. Other notable developments include the development of the Standard Template Construct (STC) system and the artificially-intelligent Men of Iron, powerful combat robots.
The Age of Technology ended in inter-human war and anarchy, in an era known as the Age of Strife, as massive Warp storms cut off interstellar travel and communications across the whole of the human-settled galaxy. The STC systems lapsed into disuse or decayed leaving entire colonized planets stuck and unable to perform interplanetary travel. In a relatively short span of time, the once galaxy-spanning human civilization was brought to its knees, and was forced to endure nearly five millennia of anarchy, terror, war, genocide and slavery. Other than tales of great suffering, little information has survived this dark time to be known to the men and women of the Imperium.
With the help of the tech-priests of Mars, the Emperor created the Astronomican, a supremely powerful psychic navigational beacon powered by the Emperor's own will and psychic abilities that would allow simplified and safer interstellar travel through the Warp across far greater distances than before, which he would use to unify the lost bastions of humanity scattered across the cosmos. To assist in his Great Crusade, the Emperor used his DNA to create the legions of superhuman, genetically-engineered warriors that came to be known as Adeptus Startes, the Space Marines. The process started by designing 20 clone-sons from his own genetic code to serve as generals for his army known as Primarchs - they were transhuman demigods born to conquer lesser beings and perfect to lead the Emperor crusades. The Chaos Gods however sensed that their enemy's plans would be too successful, the Chaos Gods cast the Primarchs into the Warp, landing them across several different planets. Nonethless, the Father of Mankind devised a new plan and used the geneseed of his sons to create his super soldiers and started the Great Crusade without them.
The Horus Heresy
As his campaign to unite mankind proceeded, the Emperor reunited with his sons one after the other, who have rose into dominance and conquered the worlds they landed upon. Most favored of them all was Horus Lupercal, the very first to be recovered. In the two hundred years that followed, Primarch after Primarch were reunited with their father, the Crusade grew larger and countless xeno races were purged and driven out and all human populated worlds were united under the Emperor's peace.
When humanity's triumph seemed inevitable, the Emperor returned to Holy Terra and left his son Horus in command of the Great Crusade, naming him Warmaster with full authority over his other fellow Primarchs. He established the Imperial Truth -- a rationalist, atheistic faith in science and technological progress that rejected all the vestiges of human irrationality and superstition, including all forms of religious faith. He was staunchly atheist and much to his chagrin, was considered a god by his followers despite, among other things, being considered the most powerful psyker of all time, capable of bending the fabric of reality as he saw fit - his power was considered godlike, though he insisted otherwise. By the time of the Great Crusade he already had purged all of Terra's ancient religions, not only for deeming it the reason behind humanity's plight, but because belief was tied with the entities of the Warp and in a effort to starve them off worship. His anti-religion policy extended even to worship of his own figure, going as far as to severely punish his own son Lorgar Aurelian, who had established the worship of the God-Emperor, by destroying the temple-city of Monarchia, forcing Lorgar and his soldiers to kneel in its ashes.
The Emperor's own disconnection from mankind, his distant treatment of his sons and arrogance ultimately lead to his own undoing. Horus, felt that resentment of his father taking credit for his own victories, while Lorgar, whose faith was completely shattered, turned to a new deity to worship: Chaos. Lorgar ended up leading Horus astray as well, who then spread its taint across his men. Before anyone noticed, half the Primarchs were corrupted and sided with Horus in a conflict that came to be known as the Horus Heresy, the most terrible conflict in the history of the Imperium. The Emperor was forced to kill Horus but was mortally wounded in the battle, and his last acts were to give instructions to complete the Golden Throne, massive cybernetic life support mechanism utilizing ancient advanced biomechanical technology that possesses the ability to amplify psychic abilities. The Golden Throne now holds the desiccated and slowly decaying body of the Emperor in stasis, and preserves His mind and will, which originates and guides the psychic beacon that is the Astronomican within the Warp. He is also said to constantly struggle to keep the forces of the Ruinous Powers of Chaos at bay so that humanity can flourish even to the extent that it has in the galaxy it shudders closer to collapse. As the Imperial Creed has taught for over 10,000 standard years, the Emperor protects...
Regarded as the perfect human in every possible way, the Emperor was viewed as a wise leader, the savior and protector of mankind who lead them from darkness, who watches over them and protects against the Forces of Chaos and Xenos. He is the Holy Spirit, the Giver of Life and the Guardian of Earth. No one truly knew the man himself however, except his chief advisor and confident Malcador the Sigillite. Upon further inspection of his character, one would find him a very complex and flawed individual than His worshipers could ever believe.
One thing that could be said for certain about him is that every action he took, no matter how questionable from a moral or practical standpoint, was for the betterment and advancement of his race. The Emperor was fervently atheist - while he acknowledged the existence of Warp entities, he refused to acknowledge them as "Gods" worth being worshiped. He proposed rational explanations in place of superstition, as there never was a question he could never answer through application of his intellect for as long as he lived. Believing that religion caused most of humanity's misery as well as it fueling the Ruinous Powers, he sought to completely erase faith in general to starve them out completely of power. The Emperor also disapproved worship of his own person, as it went against the Imperial Truth, his plan for humanity to be utopia of science and reason. He preached for reason and logic in place of belief, he could be just as intolerant and bigoted as the zealots he condemns. His victims, both humans and aliens, outnumber those of all of humanities dictators in history up to that point combined. Entire cultures were crushed for refusing to submit to his rule, even peaceful xeno species such as the Interex - one of the few with the knowledge about how to fight the Chaos Gods and could have been potential allies - were all wiped out in the name of humanity's superiority.
The Emperor's fatal flaw turned out to be his hubris. His intellect and wisdom made him believe he knew better than absolutely everyone and his will should never be questioned because everything he does will work out in the long run. His arrogance made him underestimate the Ruinous Powers of the Warp, His plan to starve out the Chaos Gods by suppressing religion would have failed, because its not just worship that sustains their existence, but also raw emotions. The Immaterial is made from all living beings' collective consciousness, so emotions that are particularly strong gain form and sentience which created the Chaos Gods in the first place. Even if the Emperor succeeded in wiping out all faiths completely, their shadow would still loom over the material world.
Another product of his hubris and a major factor that lead to his downfall was his inability to relate with other beings, whether if it was his subjects or his own sons. Truly, the Emperor sincerely believed in serving mankind's well being, but because of his extremely advanced age and unparalleled power, he was detached from everybody else and viewed them as his inferiors. Keeping vital information to himself was very in-character, as due to his infinite wisdom, he didn't think those beneath him were either trustworthy, wise or capable enough to share it with them, he didn't think they would be able to comprehend his works.
Finally, he made a mistake in disregarding the human need to believe in something greater than oneself, and despite his best efforts with the Imperial Truth reason and logic simply weren't enough to fill the place of religion. Ironically, his solution was not to suppress faith but to redirect it towards something else, intended to be the idea of the Imperium, but because of his own unmatched psychic powers and enigmatic nature that "something else" ended up being the Emperor himself. The most tragic in this irony is that his ascendance to the Golden Throne had simultaneously ushered a age of darkness, intellectual regression, political repression, constant exploitation of the many by the few without his direct guidance and only serving as a religious figurehead, but also, his worship is the one anchor of bravery and perseverance keeping the humans together from collapsing back to their pre-Great Crusade days, it gives them hope and courage to survive in a universe which they are beset from every corner. He endures his endless pain and accept his role as a deity, because without him mankind will not survive.
In the end, the God-Emperor, for all his infinite and terrible might, ultimately proved to be about as fallible and flawed as any man.
The Emperor's Fate
By the time of the 13th Crusade, its reported that many mechanisms of the Golden Throne have developed technological failures beyond the current ability of the Tech-priests to repair. Because of this, it seems possible that the Emperor's body will die at some time in the near future. Depending on the many myths and fevered predictions that have come to dominate the Imperium's "Time of Ending," this unwelcome event will either destroy or actually save the Imperium of Man, and the galaxy as a whole, from the inevitable destruction brought by Chaos. Several scholars theorize the hypothetical scenarios and consequences of what would happen should this terrible event come to pass.
The Imperium Falls
At the barest minimum of all negative scenarios, with the Emperor dead there will be no one left to power up the Astronomican, the device used to allow interstellar travel among planets. All planets would have been left stranded and unable to interact with each other, leaving them vulnerable to Chaos incursions and Xeno invasions. It would have been impossible to call for reinforcements in case of an attack, the inhabitants would have been left to fend for themselves and they would quickly revert to the state they were during the Age of Strife. That is considered the least horrifying of all cases should the Emperor die.
A New Eye of Terror
The Eldar say that in the event the Emperor dies, a new Eye of Terror will be created in the center of Earth, plunging the planet and all surrounding worlds into the Warp. This theory is supported by the fact a very large Warp rift was opened inside the Imperial Palace during the Horus Heresy and the Emperor had to spend all of his psychic forces to close it, or at least keep it from getting any bigger. Even now, 10,000 years later, the Warp exists and the Emperor fights to keep it closed. Not only that, should the Emperor pass away entirely, his soul would have been complete in the Warp and rise as a new deity with infinite power, superior to all Chaos Gods combined. 50/50 chances says he would either turned into a God of Order and lead mankind into victory or become a fifth Chaos God.
The Star Child
An even more obscure theory with two separate aspects claims that when the Emperor unleashed the psychic wave that destroyed Horus, he sent a small part of himself to the Warp - this little fragment is considered the Star Child; an being waiting to be born or reincarnated into human flesh the moment his original body dies. The second aspect spouses that in over the 50,000 years he lived, the Emperor formed many families and fathered thousands of children. His male descendants have inherited direct portions of the Emperor's genome and they are immortal like their father, though unlike him they are sterile in every case. His female descendants are simply normal human women, though they may exhibit potent psychic abilities, particularly forms of precognition. A hidden group within the Imperium that call themselves the Illuminati know of the existence of the Emperor's scions and plan to gather them together and sacrifice them before their corpse in order to renew his essence and be reborn as a legitimate living God-Emperor. This theory is disregarded by the Ecclesiarchy and the Inquisition at large as heresy of the most vile caliber, and the supposed group identified as Illuminati to be Chaos Cultists of Tzeentch subtly working to undermine the Imperium from within. However, there is a faction within the Inquisition known as Thorianism, who is investigating the possibility to bring the Emperor back by searching for his consciousness and place it under a physical vessel to restore him back to life. Critics to Thorianism perceive this as a dangerous idea, not only due to the other possibilities making it not worth the risk, but bringing the Emperor back would split the Imperium between the skeptics of the Imperial Truth of the original Empire and the believers of the Faith.
There is the existence of human individuals known as Perpetuals, who are effectively immortals and capable of resurrecting themselves in case of death and its believed by certain people that the Emperor to be one as well. The evidence to support this is that one of his Primarch sons Vulkan, who had inherited traits of his father just like his brothers but exclusive to each other, happened to be a Perpetual who was captured by the servants of Chaos and subjected to hauntingly visceral tortures that killed him multiple times, but he kept coming back every time he died. Theoretically speaking, should the Emperor's physical body being allowed to pass away, he would return to life in a matter of hours. This seems purely conjectural however, as the Perpetuals' existence is dismissed by the Imperium and the individual cases are not documented in depth. The known Perpetuals to exist also are immortal under different circumstances such as John Grammaticus, who was artificially given immortality by a secret group, while the Emperor became immortal naturally thanks to his vast psyker powers.
Powers & Abilities
The Emperor is an Psyker - an individual with psychic abilities that draw their powers from the Warp - of immeasurable level. A base psyker can read and control minds, levitate, control elements and perform what some people would regard to be sorcery. The Imperium ranks the Psyker's most powerful level as Alpha Plus, described as being able to "turn a man inside-out with a glance", "snap a Battle Titan in half with a flick of the wrist", and "a muttered syllable can turn an army upon itself in a frenzy of blood lust". They are capable of destroying entire worlds -- sometimes unintentionally. The Emperor's own power is so massive that it cannot be graded by any standard, though he has never performed such a feat. The greatest demonstration of his power was at the end of the Horus Heresy, where he unleashed a psychic wave so massive that banished every Daemon on Terra, completely obliterated Horus' soul and conscious in a way he can never be resurrected and severely assaulted the Gods of Chaos across the Warp.
Unlike most individual Primarchs and Space Marines who were merely long-lived, the Emperor was truly immortal - having not aged past his physical prime and being over 38.000 years old before his ascendance to the Golden Throne. His immortality allowed him to hone his psyker powers and his intellect beyond any genius could hope to achieve. He possessed a superhuman physique, having a body that is two or three times the size of a human being and empowered with vast physical strength and stamina, which was later reflected on his sons and the Space Marines in general. Though he ultimately proved to not being completely invincible due to being mortally wounded in his fight with Horus, it should be noted his opponent was none other than a formidable demigod of his own right, backed the four Gods of Chaos and Emperor also held back his own power, as he hesitated to strike down his favorite son with all his full might.
After the events of the Horus Heresy, his body was shattered from fighting his son Horus and he had to be put in the Golden Throne to sustain his mind. After thousands of years, though his physical body is now more corpse than man, the effect of trillions of human beings expressing a deep faith in his divinity has massively empowered the Emperor's mind and soul within the psychically-reactive Immaterium, where reality is shaped by the collective beliefs and unconscious desires of the galaxy's most populous intelligent species. Whatever he may have been before the Horus Heresy, the Emperor now truly is a God within the Warp, equal in power to any one of the four major Chaos Gods, and very likely as powerful as all four of them combined, as he has become perhaps the strongest spiritual force for Order in the Milky Way Galaxy. The downside to this is that he has been fully conscious this entire time for ten thousands of years, trapped in the charred husk his body has became, unable to die and his existence is one of endless pain and suffering, that it is only his utter devotion to the human race that keeps him from accepting the death he now desperately longs to embrace. Another downside is that it requires exactly 1,000 souls being sacrificed daily so it can power its psychic connection with the Astronomican, the warp-beacon that allows Imperial ships to navigate galaxy-spanning distances. Should this connection ever go down, long-range interstellar travel would become impossible for humanity and the Imperium would fall apart.
The Emperor was also a skilled statesman, military leader, philosopher, scientist with thousands of years worth of knowledge and experience in all fields known to man. Chiefest among his achievements was the invention of Astronomican and the Primarch project, which subsequently created the Space Marines.