As of the current lore of Warhammer 40,000, the Emperor of Man is shattered husk of a man on the Golden Throne. Even though his body can no longer sustain life, his mind carries on with the sacrifices of 1000 Psykers a day and the sheer vigilance to stop chaos from destroying the Imperium of Man.
Not much is known about the Emperor before he unified Terra and the rest of humanity, except that he was an ancient man, who lived many lives. He was the first of many psykers or shamans as they were known back then. In that time, he mostly watched as humanity gave into the temptations and beliefs of the chaos gods. Then as the years went on he decided to take a more direct approach to helping humanity. As his powers grew, so was his ability to unify those around him. As the millenniums passed however, betrayal and horror would befall him.
The Great Crusade
The most ancient records only go back as far as pre-unification of Terra (Humanity's home world, aka Earth). His beginning was that of a warlord among many who sought to rule all of Terra, and in the end he was the sole victor. Throughout these unification wars, he was able to create the first genetically engineered super soldiers and was able to unify all that opposed him. Shortly after, he set his sights on the stars and with the help of the Adeptus Mechanicus (A cult following a presumed machine-god, situated on Mars) was able to create the vessels to start what became known as the Great Crusade, aiming to unify all of humanity.During this time the Emperor had created the Primarchs, sown from his very own genes. Every chapter had one Primarch and the "gene-seed" based on the Primarch's own, unique genetic code. Though as the Emperor was busy preparing for the Primarchs and their legions to set out into the stars, the Chaos gods saw perhaps opportunity, or the dangers of what the Emperor had planned. As such, they somehow managed to scatter the Primarch vats, tubes in which the demi-gods were to grow, across the galaxy. With his sons warped to places unknown, and thus his generals missing, it was a major setback for the Emperor and his plans to unite all of humanity.
Still, the Emperor still set forth from Terra to claim all the outer human worlds under one banner and destroy any opposition in his path, this time aided by his trusted Space Marines, created by utilizing the gene-seed left behind by his Primarch sons. In the end, the Emperor would reunite with all of his sons but two, who to this day remain a mystery along with their legions, records of them removed a long time ago from the Imperial databases. A total of 18 were found with each having their own set of traits and abilities to contribute to the crusade - and with their Legions at their command, in a way, their sons, the Imperium of Man seemed nigh unstoppable.
As the the empire reached it's apex, a million worlds had been conquered and humanity seemed to stand before yet another golden age, unified under the gaze of the Emperor. Though unknown to the Emperor, Horus, his most beloved son, would fall to the corrupting influence of the four chaos gods, and in turn have more follow in his footsteps. During a series of trying events (even for a Primarch) Horus was ultimately led astray by the Chaos gods onto the path of corruption, believing whole-heartedly that his father had forsaken him through numerous visions of supposed future events. Horus, having been appointed Warmaster for the Crusade with the Emperor returning to Terra, naturally let his influense spread to any, and all chapters in his vicinity. At first slow, he became more and more ruthless until he simply purged all within his own legion, and the others following him, that remained loyal to the Emperor and would refuse to turn to his side. A grand total of 9 other chapters and their Primarchs betrayed the Emperor (Although it is uncertain in the Alpha Legion's case) and fell to the corruption of chaos through various means.
After the betrayal of so many of his sons, civil war broke out within the Imperium. Horus and his newly renamed legion, the Sons of Horus took siege of Terra along with several other legions. In the first 30 days of fighting the orbital defenses were gone and heavy bombardment pelted the planets surface. The defending loyalist chapters of the Imperial Fists, Blood Angels and White Scars were heavily outnumbered and the fighting soon turned to the siege of the Imperial Palace. On the 55th day of the planet's siege, the traitors penetrated the outer wall. By that time, Horus got word of other loyalist legions on their way to reinforce the Emperor, The Ultramarines were pushing their way towards Terra, The Space Wolves and the Dark Angels following in their wake. No doubt realizing that this would turn the odds against him, Horus dropped the shields protecting his battle barge, the Emperor immediately taking the chance to teleport inside, along two of his loyal Primarchs. Ironically, both the Emperor and Horus at this point hoped to end this quickly.
The fighting was chaotic, taking place all over Horus ship as the teleporter scattered the Emperor's forces all across the barge. The Primarchs accompanying him, Rogal Dorn and Sanguinius also found themselves separated from their father. After the battle on was over, Horus was defeated and the siege of Terra ended with the Traitor Legions fleeing the planet.
This victory however did not come without a price, Sanguinius having been slain as he attempted to reason with and ultimately stop the power-infused Horus, all four Chaos gods channeling their might into him. Ultimately, the Emperor destroyed Horus using his psychic powers, shattering the Primarch's soul, but not without first having been critically wounded. Due to his love and compassion for Horus, his first and foremost of sons, even the Emperor had hesitated long enough to sustain life-threatening injuries. Rogal Dorn arrived to the battle last and although he didn't fight, he was able to carry out the Emperor's last will as the dying god gave Dorn instructions of how to install his broken body onto the Golden Throne - a majestic throne built by the Emperor on which he would normaly sit, channeling his power to act as a beacon of light, a compass of sorts, for those vessels traveling the dangers of warp space.
The Golden Throne
In the direct aftermath of Horus death, the Emperor was placed on The Golden Throne. Rogal Dorn, himself, installed the Emperor onto it; the throne acting as a large, complex life-support machine. Even though the Emperor had been critically wounded, this machine is able to prevent him from ever truly dying. His body can no longer sustain life, but his mind is still very much active, standing eternally vigiliant against the forces of chaos, and is said to be the one thing that keeps the chaos gods from simply outright destroying the Imperium. To help sustain his mind, 1000 psykers are sacrificed per day to prevent him from perishing, nourishment to the ascended god's soul. Some say the Emperor will return one day and usher in a new age for the Imperium, seeking revenge for the injustices that happened so many millennia ago.
As of 999.M41 (the last year of the present millennium), the Adeptus Mechanicus have discovered irreparable flaws in the Throne that could ultimately endanger the Emperor's 'life'.
As of now, the Emperor's broken body sits on his Golden Throne, ever vigilant and keeping a watchful mind over the citizens of the Imperium. There are those who pray to him for the salvation and peace that he offers - particularly those who spill their blood for him. From the Emperor's Hammer; the Imperial Guard, to the remains of the God-Emperor's legacy; the super soldiers of the Space Marines, prayers and praise to his existence is like an ever-present, resounding chant across the Imperium of Man.
As they all wait for his return, the High Lords of Terra pose as the governing body for the Imperium, nine leaders from every major group around the galaxy. Their duty is to keep order until He returns and guides them to a more prosperous future.
In the grim times of the 41:st millenia, everyone needs something to hold on to, and a reason to carry on.