The first race to reach space-fairing status in the galaxy was known only as the Old Ones, though their heritage is unknown it is likely they were of reptilian decent (the Old Slaan). Reaching the peak of science they traveled the galaxy and seeded new or nurtured existing life, in this way many young races came into being including the Kork (Orks), Eldar and even Humanity. They achieved this with their formidable understanding of the parallel dimension known as the Warp, a universe made of pure shifting energies where time and distance had little or no meaning. In this way a starship could travel thousands of light years in a very short space of time. However as the warp was subject to “tides” an “currents” ships could be blown off course or experience erratic journey times, therefore the Old ones constructed the Webway, a system of “tunnels” through warp space. These linked all the worlds of the Old Ones, essentially eliminating the need for conventional space travel.
The second race to advance was known as the Necrontyr, a humanoid race who suffered short and horrible lives due to their close proximity to a particularly violent star. To combat this the Necrontyr quickly advanced in science to try to extend their lives, foremost of their achievements was a kind of “living metal” from which they made their starships. However having limited understanding of the warp their progress across the galaxy was slow. Tensions within the ruling classes of the Necrontyr frayed and inter faction war became commonplace. To counter this the Necrontyr leaders engineered a war against the Old Ones as a way to try and unite their race. This however was a war they could never hope to win, as the Old Ones were able to outmaneuver them at every turn with their warp technology.
With their defeat the Necrontyr were banished to the other side of the galaxy and inter faction war threatened to engulf the Necrontyr yet again. In desperation they looked around for a new solution and found the C’tan. The C’tan were a race of energy beings who survived by feeding off raw star energy, the Necrontyr were able to make them physical bodies made from their living metal. However it was then they realized their huge error, the C’tan quickly started to feast on the souls of the Necrontyr as they found them far more “tasty” than raw star energy. One C’tan (later known as the Deceiver for this very act) presented the Necrontyr with a solution involving transplanting their souls into similar living metal bodies as the C’tan. The Necrontyr agreed, however the process of transference robbed many of the Necrontyr of their minds, instead becoming the slave army of the C’tan. Those who retained their mind secretly cursed the C’tan for this act and plotted their revenge in secret.
The War in Heaven
With their new army of Necrons, the C’tan made ready for a war upon the old ones in search of new souls to consume. The following conflict (sometimes known as the war in heaven) was of a scale so huge than no war after could ever hope to match its ferocity. The war itself lasted for millennia and slowly but surely the Old Ones were pushed back across the galaxy. However the C’tan did possess one main weakness in the form of the warp. The Old Ones were forced to use every warp related weapon available to them to stem the assault of the C’tan. This included bio-engineering races with a high warp affinity to combat the C’tan including the Eldar (perfect in all forms of psychic warfare) and the Orks (perfect in all forms of physical warfare, whilst retaining a high warp affinity). It is likely the old ones experimented with early humanity, however they were never able to finish their work.
After millennia of fighting the Old Ones were all but defeated. Just as the C’tan sensed victory and were at their weakest, the Necrons sprung their trap. The weapon they deployed succeed in shattering most of the C’tan into “shards” and scattering them over the galaxy, breaking their power forever. Just as the dust was settling a new and terrible enemy presented itself known as the Enslavers. The immense emotional pressure displayed during the war in heaven had manifested in the warp as a race of large jellyfish like creatures who feasted on all organic life and destroyed the rest. Weakened as they were, none of the races (particularly the Necrons) were able to combat this galactic wide incursion and all were forced into hiding, any remaining Old Ones were surely destroyed.
After many years, staved of their food the enslavers finally retreated leaving the young races free to reclaim the galaxy. The Orks and particularly Eldar were able to quickly spread themselves over the galaxy during this period; the Eldar inherited the broken remains of the Old Ones Webway system. As both races expanded so did their influence on the warp, eventually manifesting into gods which were suited their races character (the entire Eldar Pantheon and Gork and Mork). Sometime during this period the Eldar underwent a large civil war, reflecting the war that the Eldar Pantheon experienced in the warp.
Rise of Humanity
Meanwhile Humanity was left to develop relatively undisturbed on the far side of the galaxy. During humanities pre-history the race was led by many psykers known as shamans. The shamans had the ability to retain consciousness after death within the warp and thus be safely re-incarnated into new bodies. However as time progressed this process became less and less safe and more and more shamans were unable to return as a result. The shamans predicted that this disturbance in the warp would eventually manifest itself into a new and terrible power and without their guidance humanity would surely perish. Therefore as one all the shamans committed suicide at the same time allowing all their spirits to coalesce within the warp. Exactly one year after the sacrifice a boy was born who inherited the great soul, this boy would one day be known only as the Emperor.
The Emperor set about guiding humanity from the shadows and over the course of millennia took the guise of many religious and political leaders, never revealing his true identity. Despite his best efforts the emotions displayed by humanity (and the galaxies other races to an extent) eventually formed the first three gods of chaos within the warp: Khorne, Nurgle and Tzeench. Due to the small amount of humans at the time these gods were very weak, however the Emperor knew that with humanities growth, so the power of the gods of chaos would grow with them. Shortly after this the Emperor (in the guise of a knight) encountered the slumbering form of a C’tan in the Libyan Desert known as the Void Dragon. Due to the C’tan’s huge power the emperor was unable to slay the beast but was able to subdue it, hoping it might prove useful in his plan for humanity.
Over time humanity spread out into space, however without warp technology progress was slow. The Emperor imprisoned the Void Dragon under the surface of Mars, its psychic power influencing generations of Martian colonists. This lead to greatly accelerated technological understanding from mars, eventually forming the Cult Mechanicus who worshiped technology (the Omnisiah) as divine. It was not until around the year 15000 that humanity discovered the warp drive and the mutant individuals (known as Navigators) who could effectively pilot a ship safely through warp space. This lead to years of unprecedented expansion from the Sol system and increases in technological understanding, this was the start of the period known as the Golden Age of Technology.
The Golden Age
With this expansion humanity first encountered other alien races and partook in the first Xenos conflicts. Many individual empires formed over the years with differing approaches to relations with Xenos, however the growing Eldar Empire mostly ignored the growing human Empire as little more than a nuisance, a tiny development of a race little better than monkeys in their eyes. Core to the human expansion was a vast database of technology known as Standard Template Construct. Colonists would take a copy of the STC database which would provide them with instructions of how to build almost any technology from the resources available, in this way all colonies were able to retain a high level of technology. The STC system allowed the construction of great war machines known as Titans to defend humanities distant colonies. In all their endeavors humans were aided by a race of robot slaves known as the Men of Iron. Eventually almost all the work in the human Empire (including warfare) was performed solely by the Men of Iron. At one point however the Men of Iron turned on their former masters (Necron or Chaos influence could be the cause) resulting in a massive bloody conflict that raged on for hundreds of years. Eventually humanity was victorious but at a great cost, no self-thinking machine would ever be constructed without at least some biological components. The cyborg servitors therefore became humanities new workforce and humanities view on AI was forever changed.
The Age of Strife
The aftermath of this war as well as the increasing appearance of mutant humans known as Psykers lead to a new chapter in humanities history known as the Age of Strife. The Eldar Empire meanwhile had expanded to become the major power within the galaxy; their arrogance was such that all other alien races were beneath their notice. Their god like technology allowed them to eliminate all forms of work, including war. Their society was such that all activity was geared purely toward pleasure seeking, over time their acts started to become depraved and sickening. Due to their immense psychic presence, the warp was becoming increasingly disturbed and volatile, their emotions feeding the gods of chaos. This lead to chaos within the human Empire, as the warp disturbances made warp travel almost impossible isolating all human worlds from each other. Any thought of a unified human empire quickly vanished and many human colonies regressed back to barbarism. Psykers started to appear unchecked on almost every human world and without proper training acted as gateways for the demonic denizens of the warp to find their way into the material universe, hundreds of worlds were made lifeless from demonic infestation.
Fall of the Eldar
As the acts of the Eldar became more and more depraved so did their emotional influence in the warp. Eventually their influence reached “critical mass” within the warp and lead to the birth of the fourth god of chaos, Slaanesh. This however was not a gentle “coming of sentience” like all other proceeding gods, this was a violent birth of titanic proportions. The birth of Slaanesh rent a hole in reality right at the heart of the Eldar Empire, forming the Eye of Terror and destroying almost all of the Eldar in an instant. Furthermore Slaanesh fought and defeated the majority of the Eldar Pantheon, leaving only their laughing god (who hid in the Webway) and their godess of healing (who was captured by Nurgle). Khaine, the Eldar war god was shattered into a thousand pieces that came to rest at the heart of every craft world. These were great planet sized vessels, which sheltered the remnants of the Eldar race from the birth of Slaanesh.
Not without a sense of irony, the destruction of the Eldar allowed the rebirth of humanity. The warp storms that had persisted form millennia were blown away by the force of the birth of Slaanesh and allowed the re-connection of the human colonies. The Emperor observing the birth of Slaanesh decided that Chaos was becoming too large of a threat and reasoned he should take matters into his own hands. Proclaiming himself as the Emperor of Terra he set about work on his first generation of genetically engineered super soldiers. With these he was able to unite the warring factions of Terra under one banner and set about work on phase two of his plan. The Emperor started work on twenty extraordinary individuals, made from his very own genetic code and extensive use of warp magic. The powers of Chaos sensing the huge potential within these individuals sent agents to destroy them while still in their infancy. However at the last moment the Emperor intervened and was able to save his sons from destruction and was able to guide them to safe planets after the agents of chaos scattered them within the warp. Some of these “Primarchs” capsules became damaged within the warp, leading to mutation or corruption within some of the infantile Primarchs.
The Great Crusade
The Emperor undaunted by this situation was able to use the genetic data from his Primarchs to create twenty legions of new super soldiers he called the Adeptus Astartes or the Space Marines. With his legions he set out to re-unite mankind’s lost colonies, starting with Mars. Whilst the Emperor endeavored to spread a secular message across the galaxy to prevent worship of the chaos gods he made an exception with the Cult Mechanicus on Mars to save time, the two-headed eagle symbol represented the unification of Terra and Mars and became the symbol of the new Imperium of Man.
As this “Great Crusade” continued, the Astartes legions were re-united with their Primarchs who had risen to prominence on their home worlds due to their super-human characteristics. The fate of two Primarchs and their respective legions is unknown, however it is suggested one may have been destroyed by the Space Wolves legion and the other integrated into the Ultramarines legion. One legion’s actions were troublesome for the Emperor, the Word Bearers were spreading the word of the Emperors divinity. Keen to quash this message (and with an act of poor judgement) he brutally disciplined the Word Bearers and their Primarch Lorgar. Disillusioned by this rejection of their efforts, Lorgar and his legion looked around for a new universal truth. Their search brought them to the Eye of Terror where they discovered chaos and became corrupted by their new gods. Lorgar hoped one day to spread the message of chaos throughout the galaxy and began to engineer a plot to make it so. The Emperor was also forced to discipline the Thousand Sons legion led by Magnus the Red for excessive use of warp magic (despite best intentions). At the council of Nikea the use of psyker warriors within the Astartes legions was forever forbidden. This served to greatly divide the opinions of many legions over the use of psychic abilities.
The Emperor decided to return to Terra to execute the final stage of his plan and named Primarch Horus as Warmaster in his stead. With an act of poor judgment the Emperor thought it best not to explain the reasoning of his return to Terra to Horus.
The Horus Heresy
The Emperor began work on the Golden Throne project on Terra, a device designed to link into the Webway (and perhaps even create new sections) and thus release humanities reliance on warp travel. Horus however felt abandoned and Lorgar was able to use this feeling to manipulate Horus into believing the Emperor was planning on proclaiming himself a god. A scheme of Lorgar saw Horus mortally wounded by a warp corrupted blade and in the trance brought on by the wound was fully corrupted by chaos and the tireless efforts of Erebus, dark chaplain of the Word Bearers.
Magnus the Red attempted to save Horus during the trance but was ultimately unsuccessful. Magnus seeing that the corruption of Horus was imminent endeavored to warn the Emperor before it was too late, however his psychic message unwittingly destroyed the fragile and irreplaceable mechanisms of the golden throne and Magnus was horrified for what he had done. The Emperor thinking Magnus corrupted sent Primarch of the Space Wolves legion to bring Magnus into custody, however the corrupted Horus was able to use the schism between the two legions to persuade the Space Wolves into fully destroying the Thousand Sons. Magnus saddened by the destruction of his legion and threat of immanent and uncontrollable flesh change mutations made a pact with the chaos god Tzeench to save his legion. The remnants of the thousand sons were saved but forever enslaved to the will of Tzeench.
Horus meanwhile endeavored to overthrow the Emperor and proclaim himself new ruler. Managing to secure the loyalties of half of the astartes legions he set about ridding himself of the loyalist elements of these legions in the Isstivan system and laid a trap that almost wiped out the Iron hands, Salamanders and Raven Guard legions to a man. Worst hit was the Iron hands legion who’s Primarch, Ferrus Manus was slain by the possessed Primarch of the Emperors Children, Fulgrim. After the betrayal at Isstivan Horus’ rebellion spread all across the galaxy, different factions warring over allegiance to the Emperor or Horus. The rebellion eventually reached Terra itself where the full might of the traitor legions bore down upon the few surviving loyalists. Believing himself strong enough, Horus let the shields down on his starship and challenged the Emperor to single combat. The Emperor with a contingent of loyalists and his sons Rogal Dorn and Sanguinius teleported onto Horus’ flagship. However the teleportation was disrupted and the loyalist forces were scattered throughout the ship. Sanguinius reached Horus first and tried to reason with him, unfortunately he was unsuccessful and was slain by Horus. The Emperor then reached Horus and proceeded to engage in a duel, however the Emperor believing Horus could still be saved held back and was seriously injured as a result. Just as Horus was about to deliver the killing blow a guardsman/terminator/custodian entered the chamber who Horus tore apart with a single glance. The Emperor seeing Horus could not be saved utterly obliterated Horus’ soul with the last of his psychic power, Rogal Dorn eventually found the wounded form of the Emperor and bore him back to Terra. The Emperor instructed Dorn how to convert the golden throne into a life support machine and the Emperor was laid to rest there, neither alive nor dead, his spirit constantly warring within the warp to prevent mass demonic incursion into the galaxy. With the death of Horus the traitors retreated to the eye of terror under the new leadership of first captain Abbadon. The remaining traitor Primarchs by this stage were fully corrupted into daemonic champions of their respective gods.
The New Imperium
Roboute Guilliman, Primarch of the Ultramarines (the largest and least affected loyalist legion) took over temporary command from the emperor and over the course of many years set about re-unifying the Imperium. In this period he unveiled a great tome known as the Codex Astartes, which contained edicts on how to re-unify the Imperium. Core to this was that all remaining loyalist legions should be broken down small independent army groups known as chapters to aid the defense of many fronts. While there was initially anger from some of the other Primarchs his edict was eventually carried out in an event known as the second founding. In the years after, all the remaining loyalist Primarchs were either killed or disappeared into legend. With sense of irony, worship of the Emperor became the official religion of the Imperium under the huge organization known as the Ecclesiarchy and the Inquisition was founded to ensure the loyalty of imperial subjects and to root out the taint of Daemos and Xenos. Leadership of the Imperium was given over to the council of the high lords of Terra.
In the ten thousand years since the Horus Heresy the galaxy has been in a state of total war. By the strict edicts of the Mechanicum technology (although roughly constant) has become mysterious and not fully understood leading to almost no technological advancement in ten thousand years. About 5000 years after the Heresy the Imperium was once again plunged into total civil war when confrontations between the Ecclesiarchy and the Administratum reached a peak. Out of the turmoil the mad High lord Vandire took control of the Ecclesiarchy and ruled the Imperium with a madman’s iron grip. Eventually order was restored when Sebastian Thor (thought to be an avatar of the Emperor) was able to restore order to the Imperium through strength of arms and miraculous unforeseen happenings (such as the creation of the storm of the Emperors wrath). The Imperium has endured 12 of Abbadons black crusades as well as the largest Ork Waaagh since Ulanor. In the Last days of the 41st millennium a new race of warp resistant Xenos known as the Tau have come to the fore on the fringes of the imperium. A threat perhaps bigger than Chaos itself has also presented itself in the form of the Tyranids, vast fleets of extragalactic insectoids whose sole goal is the consumption of all biomatter within the galaxy. At long last the Necrons are emerging from their Eons long slumber, ready to reforge the one glorious Necron Empire and rid themselves of their cold metal bodies. It is the 41st millennium and there is only war.
-credit to vodo40k for his awesome, awesome summary ;).