Since it's the most interesting thing this thread has talked about in months and isn't another permutation on "which horoscope sign would the Primarchs have", I'm going to post some more about my thoughts for the factions and timeline of Only Peace.
Timeline
Early M42: Gathering Storm, Dark Imperium, partial Human-Eldar alliance.
Mid M42: Guilliman's reforms set in, Imperium Secundus falling despite hard fought pathways being maintained, Tau initiate geometric expansion, Eye of Terror 150% size at the Fall of Cadia, final Tyrannid scouting fleets arriving, Octarius War resolves in Ork victory.
Late M42: Mass Necron awakenings, Mechanicus obtains pylon tech, Imperium Secundus lost outside of Ultramar, extreme conflict in Tau-Necron-Ork-Tyranid clusterfuck, Daemon Princes and surviving Primarchs all emerged, galaxy-wide Ork exodus towards Tyranid zones, Dark Eldar civil war (by their standards).
M43: Mechanicus cracks pylon tech, warpstorm expansion inhibited, contact with Imperium Secundus regained in full, partial reconquest. Angron, Mortarion, and Russ killed. Temporary break in Human-Eldar alliance due to Farseer bickering, Tau break interdiction through use of AI systems, Necrons turn efforts mostly against Tyranid incursion, Orks further driven away from human systems by pylons inhibiting WAAAGH field, Central Hive Fleet Gamchicoth arrives in the galaxy.
M44: Maelstrom sealed by pylon deployment, Segmentum Pacificus undergoes mass stripping of human life to feed warfronts after large-scale rebellion is put down, Ultramar consumed by Tyranids, all remaining Chaos Astartes groups divide to fight Imperium or Tyranids. Perturabo, Corvus, and Alpharius(?) killed. Tau war effort turned entirely against Tyranids, Exodites & lost Craftworlders flood Commorragh, Necron awakening over 99% complete, Ork species experiences religious ecstasy. Grand alliance between humans, eldar, tau, and necrons forms.
M45: The Golden Throne fails. The Emperor forces all remaining psychic energy through the Astronomicon directed at Central Hive Fleet Gamchicoth. Effect is visible in realspace, dispersing several collateral warpstorms and killing or driving mad approx. 500 million Norn Queens. Central Hive Fleet Gamchicoth critically disrupted and begins infighting, the Emperor disunites into component souls, all psykers in Sol system killed instantly including Grey Knight garrison. Realspace pylon systems begin overloading and failing, Maelstrom, Eye of Terror, and Terra-centered storm begin rapid expansion. Magnus, Khan, and Vulkan killed. Grand alliance collapses with reduction in Tyranid threat, Necron dominance in Ultima Segmentum, Tau Ethereals usurped by AI systems, Ork warbands below replacement rate, Q'Orl exterminated due to weakened defenses in Segmentum Pacificus, Craftworlder unity collapses.
M46: Gradual recoalescence of Central Hive Fleet Gamchicoth as more Norn Queens enter the galaxy and rogue Tyranids are wiped out, Terra-warpstorm sealed by overwhelming deployment of pylons, Astronomicon Choir relights at 12% efficiency, Ynnead born early due to lack of viable future pathway and self-annihilates Slaanesh with all hir followers, Khorne ascendant, Tzeentch descendant. Fulgrim and Lion El'Johnson killed, total human population at under 60% of M42. Necrons turn efforts against Tau AI systems, Ork resurgence and partial splinter back towards human systems, Craftworlder unity restored, Commorragh usurped by Harlequin troupes.
M47: Central Hive Fleet Gamchicoth's extra-galactic portions enter starvation conditions due to unplanned degree of resistance, some Norn Queens turn against the swarm or begin seeking power from Nurgle. Ecclesiarchy authority collapses, expelled from Imperial Senate by Guilliman. Segmentum Tempestus begins faltering but large advancements are made in Ultima Segmentum. Pylon systems reach all time high. Necrons successfully contain Tau AI to heavy losses.
M48: Central Hive Fleet Gamchicoth's extra-galactic portion undergoes mass loss of coherence, about half of Tyranid species dies of starvation before reaching the Milky Way. Lorgar emerges from the Eye of Terror at the helm of Chaos Undivided forces with the power of the three remaining Ruinous Powers. Major Ork warbands turn attention towards Eye of Terror. Human-Eldar forces advance against Necron dynasties, who have lost some coherence with the coming end of the Tyranid threat.
M49: Tyranid species eradicated. Pylon deployment begins to overcome the Warp on a galaxy-wide scale. Lorgar presumed dead. Imperium subjugates Tau homeworld, reconquest of Eastern Fringe and Ultramar. Ork bands experience discoherence from loss of WAAGH field. Some Necron dynasties flee to the Magellanic Clouds.
M50: The Eye of Terror closes, never to open again. Chaos Astartes all but extinct. Milky Way Necron pushed to the edge of the galaxy. Eldar-Human peace finalized, the two societies will remain separated but not interfere with one another. Craftworlds make port in Commorragh for the first time in many, many thousands of years. Orks reduced from galactic threat to segmentum threat. Total human population at under 40% of M42. Guiliman's reforms of the Imperium extend into civil society, now that such a thing exists again, recreating a degree of Great Crusade-era culture.
M51: The Warp unravels, unable to find purchase anywhere with the oppressing influence of pylon technology coating the galaxy. The Realm of Souls is restored. Whereabouts, if such a term is correct, of Khorne, Khaine, Nurgle, Isha, and Tzeentch are unknown. Cegorach lounges about in various areas of the webway, occasionally using parts of Commorragh as a throne. Few eldar choose a life outside the webway as they find their psychic potential dimmed, a fact that sends some humans into their midst as well. Milky Way Necron retreat to hidden tomb worlds and enter hibernation. Orks reduced from segmentum threat to sector threat. Guiliman found dead by his own hand before a copy of his final treatise on human society and galactic government.
M52: The Age of Silence. Total human population at 80% of M42. The Imperium has worked out into something that is not quite a dictatorship and not quite an oligarchy. Pylon systems drawn down to less resource-intensive levels. High ennui amongst human species. Mechanicus retools towards exploration, some Astartes chapters voluntarily disband, political controversy over military spending, hive world cultural renaissance. Most powerful Imperial organizations are the Adeptus Administratum, Chartist Captains, Inquisition, Adeptus Mechanicus, Adeptus Astra Telepathica, Imperial Guard, Adeptus Arbites, and Navigator Guilds in that order.
Alien Factions
Eldar: With the exception of some hardcore Exodites and followers of the Outcast paths living amongst humans, all eldar live in the Webway. The peace between humanity and the eldar survived the apocalypse, but old habits die hard and the xenophobic chauvinism between the two species has only somewhat faded. Young eldar are more critical of the peace and desire a galaxy not under psychic suppression or human dominance. Population mixing in Commorragh has weakened the long standing genetic divisions between Commorragite, Craftworlder, Exodite, and Harlequin. Within the city the strongest group remains Commorragites, the Harlequins exercise the most effective political control, the Craftworlders have a reputation for continued isolationism on their ships, and the Exodites are much put upon. Small groups of various aliens including humans continue to live in the city in relative peace, though the old habits of the Commorragites allegedly survive amongst the most ancient Kabals. As the only eldar god still up and about, Cegorach is a common target of worship, though he claims to "be retired". Isha, Khaine, and Ynnead retain cults to no effect. Vect was assassinated thousands of years ago and nobody is mentally ready to believe otherwise.
Necron: The rising of the Necron Dynasties ultimately ended in total disaster. Even their superior technology could not stand against the flood of the Tyranids and the united efforts of human and eldar. Now, the survivors are scattered amongst the outskirt stars of the Milky Way, mostly having returned to hibernation out of despair or certainty that another good million years will see the young races scattered to dust. More militant dynasties remain on active war footing and even go so far as to prey on craft that stray too far from the light of the Milky Way. The fate of the Magellanic Cloud Necron is unknown.
Ork: The time of the WAAGH!, of Gork and Mork, and of dakka n' crumpin is done. The majority of the Orkoid species are now Gretchen and the most powerful bands are Freebootaz in areas of low human habitation. Most humans know Orks as an annoying problem that some planets have and others don't rather than a serious danger. Ork religion has turned millenarianist, those Weirdboyz able to function foretelling a messiah to exceed the Beasts who will mark their rise to crump the stars once again.
Tau: Let it not be said that the Imperium is incapable of change. For while the Tau species had been marked for death many a time before the apocalypse, when the time finally came that Imperial warships came into dominance of T'au's gravity well, they and their surviving auxiliary races were spared. Perhaps it was the influence of the grand alliance, perhaps it was pity towards another species brought low by AI research, or perhaps it was Guiliman's long rule over Imperial policy, but in the end the Tau were only brought to subjugation. Tau are not even remotely equal to humans in Imperial law, and the old auxiliaries even less so, but in worlds of the Eastern Fringe there is a certain degree of tolerance and benign neglect brought on by thousands of years of human-tau interaction. The precepts of the Greater Good continue to spread as a civil ideology turned religion, hated and oppressed on some worlds but favored and apologized on others.
Tyranid: The Great Devourer devours no more. In the end, entropy was their greatest enemy. Dead hive ships of Central Hive Fleet Gamchicoth's corpse continue to flood into the plane of the Milky Way and back out into dark space, causing frequent bouts of hysteria whenever one comes within observation range of an inhabited system. But they are dead. They are always dead, having cannibalized all that they could and entered hibernation, never to reawaken. This is what the galaxy chooses to believe...but they usually have the hive ship perforated and thrown into the sun anyway. Aside from feral bioforms sometimes found on worlds that were lost and never recontacted, the only surviving Tyranids are the genestealer cults. Most threw themselves out of secrecy and into the fire of war on the urging of the hive mind during the apocalypse, but a lucky few survived by intent or by intrigue into the Age of Silence. Without the echos of the hive mind and with the knowledge that it is dead, they are as lost as any people could be. Though the 52nd Millennium is more tolerant by half than the 42nd, they are hunted and exterminated wherever they are found. The Ordo Xenos will not rest against this final threat.
Human Factions
Abhumans: With the fall of Chaos and the doctrine of the Holy Human Form, the fear of mutants has largely abrogated for stable strains. New branches have been verified by the Magos Biologis as safe, including a number of Chaos-influenced mutations which turned mundane with the stilling of the warp. Ratlings have as rotten a reputation as ever. Efforts towards enhancing Ogryn intelligence have received more attention from the Mechanicus now that they could prove useful.
Adeptus Administratum: The most powerful organization of the modern Imperium, bar none. The Administratum has finally, after thousands of years of relative peace, begin to make measurable progress on the bureaucratic backlog (the discarding of all Ecclesiarchy-related forms improved this by up to .2% per year). The tithe system has been reformed into one less likely to cause forced depopulation of entire worlds. Imperial law has made drastic improvements in intelligibility following Guiliman's mandates. There is no time better to account for the Imperium than now.
Adeptus Astartes: The lives of the Astartes are a sorry and lonely lot in the Age of Silence. Some chapters have disbanded entirely and wander the universe alone, others like the Black Templars have taken to specialized assignments within the Imperium, while some like the Marines Malevolent have been driven to neurotic extremes searching for an enemy as they speed about the galaxy to any reports of rebellion, alien attack, or mystery. The only chapters that could be said to be taking it truly well are those descended from the Ultramarines or the Salamanders, who respectively have entered governance or mundane living as successfully as Astartes can. The hunt goes on for some infamous members of the traitor legions who's fates have never been discovered, most notably Fabius Bile and Ezekyle Abbadon. Primaris Marines are even less able to adapt then their predecessors, having been born into the apocalypse without tradition or history beyond what was passed down to them.
Adeptus Astra Telepathica: The astropath service is more vital now than ever, with the light of the Astronomicon dimmed to a flicker of its former glory and the psychic potential of humanity suppressed along with the rest of the warp. Psykers who would once enter the Imperial Guard now serve as astropaths, who for the period between the death of the Emperor and the death of Chaos were constantly at risk of daemonic possession when soul binding became impossible. Most psykers serve here, with only a small portion being granted to the Adeptus Astronomica and a smaller portion still attending the other bodies of the Imperium. Fortunately for them, the newfound vitality of the organization (and the extinction of daemons) has lead to a powerful surge in psyker rights, including the League of Blackships being subjected to direct regulation from the Astra Telepathica.
Adeptus Custodes: The Custodes now do nothing but tend to the Golden Tomb, where the body of the Emperor has rested for thousands of years. Their last service beyond this was containing the daemons summoned through the Terran Warpstorm. Beneath the Imperial palace, the broken webway gate lies in darkness, surrounded by realspace pylons.
Adeptus Mechanicus: The Mechanicus have not yet truly faced the nature of their crisis. During the time of the grand alliance, the Necrons begrudgingly provided them with the technology necessary to reinforce the Void Dragon's cage, and from this they have only become more reckless in their research. The Imperium's technology is not wondrous compared to ten thousand years ago, but it is greater. The wonders are horded by the Mechanicus, in as much secrecy as they can maintain without the distractions of the apocalypse. There is little more they can learn from what they have, and they turn their eyes towards the Explorator Fleets, so that their most delirious of prizes may one day be found. The Magos try their hardest to embark on one of the limited number of Arks, such that should you visit an actual Forge World you may find yourself unable to meet anybody of genuine authority. This rather extreme level of detachment and stagnation of younger techpriests has resulted in sharp upticks in tech-heresy (the only kind of heresy, these days) and informal personality cults around those who ought to be granted the title of Magos but are denied.
Chaos Cultists: Among the Heretic Worlds, where the grand warpstorms once raged and daemon worlds once took on unholy sapience, there are humans. Some have lived there since before the apocalypse, and come from generations upon generations of mortals who's gods were very real. And even now, when the Warp is only stillness, when the gods have been lain low, that stain cannot be erased. Worshiping Chaos grants one no boons and calls down no daemons, but the traditions from time immemorial persist all the same. It is not even properly illegal, with the state of the Ecclesiarchy, and flourishes or is suppressed based on unrelated concerns alone.
Chartist Captains: The trade fleets of the Imperium were always possessed of a secret might, but in the Age of Silence their influence is known to all. Trade is now the foremost concern of most Imperial worlds, and always more is needed. More food, more industry, more spaceships, more, and there is only one way to get any of it. The Speaker of the Chartist Captains is presently considered one of the most powerful people in the entire Imperium, to the extent of having limited requisition powers over the Imperial Navy.
Ecclesiarchy: The death of the Emperor and their subsequent ejection from the Imperial Senate broke the Ecclesiarchy in a way that could not be repaired. The Adeptus Sororitas abandoned them fully, and slowly but surely the Imperial Cult slipped away as the laws protecting it were discarded for other concerns. The faith still exists, still proselytizes, still denies the words of the Primarchs, still petitions for access to the Golden Tomb...but it only delays the inevitable. The Ecclesiarch still rules from Orphelia VII, but has not been allowed to set foot on Terra in several millennia.
Imperial Guard: The Imperial Guard is immensely over-invested, and everyone knows it. Armies continue to be recruited and deployed around every inch of Imperial territory as if it were still the apocalypse, but lingering terror and paranoia prevent an effective draw down. As is, Imperial Guard armies are the most effective form of recolonization the human race has, ending their service at a depopulated world and remaining there in perpetuity.
Imperial Navy: The Navy, on the other hand, is on the verge of death by dismantling as more and more ships are reassigned to the Chartist Captains or mothballed. The Imperium simply has other concerns, and the traditions of the Navy are at risk of being lost because of it. As is, they use what political clout they have left to agitate on their own behalf about the Necrons, the Eldar, rebels, and the risk that another Tyranid fleet could come one day.
Inquisition: The Inquisition now shares few resemblances to the Inquisition of old, which lost most of its investigative potential during the apocalypse and instead served as special forces. That role then eliminated in turn, the modern Inquisition has turned inward to attempt influence of Imperial politics. At this dawn of the Imperium victorious, the winner may shape the destiny of humanity for thousands of years to come. It is thus no surprise the Inquisition is internally partitioned into an immense number of factions regarding this issue. In more official duties, the Ordo Xenos hunts the genestealers, the necrons, and minor races that pose a threat to humanity, the Ordo Hereticus is entirely focused on ending rebellion before it begins, and the Ordo Malleus has been mostly disbanded, serving now only to study warp phenomenon and ensure the pylons remain standing.
Navigator Guilds: The apocalypse was a mixed bag for the Navigator Guilds, who now need not fear corruption by the Ruinous Powers but also must perform their duties without the light of the Astonomicon and in competition with warp jump cogitators. Though the weakened Astronomicon can travel further through the stilled warp then the turbulent one, this arrangement has hemorrhaged vast quantities of wealth, and the number of surviving Navigator families is only a fraction of what it once was. More and more, they are finding themselves influenced by the Chartist Captains and the Navy instead of the reverse.
Officio Assassinorum: The assassin clades are one of the few groups in the galaxy who now face a harder task than they did during the apocalypse. There was little will to rebel in those times, when death was upon the galaxy, but now the Imperium begins to grow fat and vulnerable with victory. The cultural renaissance of the Age of Silence has not helped matters, forcing the assassins to distinguish between budding rebels and simple counterculturalists in their duties. Their work is endless, controversial, and thankless.
Sisters of Mourning: The Sororitas kept to the fight in faith even as news of the Emperor's death and the disappearance of the Astronomicon spread. They kept to the fight even as they knew a doom beyond their imagining was reality, and fought all the harder still for the sake of their forlorn hope. But now, they are no longer needed. Their duties complete, the Sororitas as an organization have shed war, with only wandering sisters continuing to carry arms. They now travel the galaxy telling and retelling the sagas of the Emperor and his sons, from as far back as is known to the end. Ironically, they have done far more than the Ecclesiarchy ever could in retaining the worshipers of the Imperial Cult, even though the two groups utterly despise one another to a degree that verges on civil war.
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