Legion Strength and Timeline
Heresy-era:
Dark Angels - 16,000 (plus about 3,000 on Caliban who follow Luther)
Emperor's Children - 11,000
Iron Warriors - 18,000
White Scars - 8,000
Space Wolves - 9,000
Imperial Fists - 15,000
Night Lords - 14,000
Blood Angels - 12,000
Iron Hands - 11,300
World Eaters - 15,000
Ultramarines - 25,000
Death Guard - 9,500
Thousand Sons - 3,000
Sons of Horus - 16,000
Word Bearers - 20,000
Salamanders - 8,900
Raven Guard - 8,500
Alpha Legion - 7,000
Total: 211,200
Modern-era (loyalists only):
Emperor's Children - 20,000
Iron Warriors - 110,000
Night Lords - 80,000
World Eaters - 90,000
Death Guard - 65,000
Thousand Sons - 35,000
Black Templars - 95,000
Word Bearers - 130,000
Alpha Legion - 85,000
Now these are subject to change as things are tweaked, but this is roughly how it stands.
Loyalist Space Marines (late-M41): 710,000
So there are 710,000 loyalist Astartes by the time the story starts, but compare this to canon where the Imperium had a 1,000 Chapters of a 1,000 Space Marines (1,000,000) so the DH Imperium is already down more than a quarter of Astartes than canon Imperium, and I'd argue the Dornian Heresy-verse is darker and more threatening in several ways. The Imperium did lose 5 loyal primarchs in the DH (the Lion, Perturabo, Konrad Curze, Horus, and Corvus Corax) compared to the HH's two (Ferrus Manus and Sanguinius). The smaller Legions meant that the rebuilding period likely took longer as new Astartes were just replacing losses so there probably wasn't positive growth for the Loyalist Legions for several decades after the Heresy.
Now once you hit, say, a century after the Heresy, then things have improved, the traitors pushed to the Eye of Terror, and the Imperium stabilized. But unlike canon Imperium which had about a 1,500 year Golden Age with few serious threats, the DH Imperium has the Ultramar Realm led by Guilliman which is consistently expanding and has a higher tech base, so the Imperium is still fighting constantly and the best weapon against Astartes is another Astartes.
Here's a rough outline on how I think the universe would turn out.
Timeline:
M31:
-the Great Crusade is launched by the Emperor of Mankind: 800.M30
-Horus is named Warmaster and Dorn is named Praetorian: 003.M31
-Dorn is corrupted by Chaos: 004.M31
-the Dornian Heresy: 005.M31-012.M31*
-the Great Scouring: 012.M31-019.M31
-the Age of Rebirth begins: 025.M31**
-the First Imperial-Ultramarine War, a massive loyalist crusade led by Fulgrim invades Ultramar, mortally wounding Guilliman who is subsequently captured: 153.M31-155.M31
-Roboute Guilliman's stasis is placed within the Purgatory Falls Sepulchre in the Imperial Palace: 156.M31
-Fulgrim disappears mysteriously aboard the Pride of Chemos: mid-300s.M31
M32:
-the War of the Beast begins, the Age of Rebirth ends: 544.M32
-the War of the Beast ends in a costly victory for the Imperium, the Emperor's Children in particular are nearly wiped out: 548.M32
-The Beheading, the Age of Longing begins: 549.M32
M34:
-Mortarion disappears combating Dark Eldar corsairs: 600s.M34
M36:
-the Plague of Unbelief sweeps through the galaxy as warp storms increase significantly and a resurgence of the Chaos Legions occurs: 421.M36
-Lorgar travels through the Imperium, reigniting faith and pushing back against the darkness: 422.M36-433.M36
-Lorgar sacrifices himself on the world of Dimmamar, eliminating the Plague of Unbelief and the Imperium recovers: 434.M36
-Goge Vandire becomes Legion Master of the Word Bearers and the new Ecclesiarch, the Age of Apostasy begins: 435.M36
-Vandire solidifies his powerbase on Terra: 435.M36-445.M36
-the Reign of Blood officially begins, the Master of the Astronomican is assassinated and his replacement is A puppet of Vandire: 445.M36
-tensions rise as Vandire calls for ever more brutal and wasteful Wars of Faith against fellow Imperial worlds, alienating many of the Legiones Astartes who remain hesitantly neutral: 450.M36-510.M36
-Sebastian Thor, a lowly legionnaire born on Dimmamar shortly after Lorgar's sacrifice, denounces Vandire and calls for his removal: 511.M36
-forces sent to apprehend Thor are instead brought to his side, swelling his ranks as many see the Emperor's Light within him: 512.M36
-the Daughters of the Emperor sect are discovered on San Leor and are secreted to Terra to act as a personal bodyguard to Vandire, renamed the Brides of the Emperor: 513.M36
-the now insane and inept Vandire declares the Emperor's Children heretics due to their lack of Chaplains and piety, the World Eaters come to their defense and are branded as apostates by Vandire: 514.M36
-a detachment of the Brides of the Emperor is sent to arrest Thor, but fail and then try to kill Thor and are subsequently slaughtered, causing more and more of the Imperium to support Thor against Vandire: 514.M36
-Sebastian Thor leads a massive fleet to Terra, made up of elements from every Space Marine Legion, the Imperial Army, Frateris Militaris, and the Mechanicus: 515.M36
-the Second Siege of Terra commences, the Brides of the Emperor are approached by the Emperor's Custodes but the squad of His protectors are killed by the misguided fanatics, soon after Thor's forces fight their way to Vandire, slaughtering the Brides to the last woman, and Thor brings the demented Vandire before the Emperor. It is unknown what occurred, but only Thor emerged, now the Ecclesiarch and Legion Master of the Word Bearers: 515.M36
-Thor purges the High Lords of Vandire's influence, and reorganizes and reforms both the Ecclesiarchy and his Legion. He establishes the Holy Synod of Terra, Colchis and Ophelia VII as well as the office of Arch-Cardinal for those respective worlds to check the Ecclesiarch's power. No single individual would ever again hold the amount of power Vandire had. Thor leads several Wars of Faith to rid the Imperium of Vandire's cronies and to beat back the resurgent Traitor Legions. The Imperium eventually stabilizes. For his last reform, Thor steps down as Ecclesiarch, stating no Word Bearer would ever hold the office again. The Word Bearers become the Chamber Militant of the Imperial Cult, and the body that ensures such corruption never takes root again. These are known collectively as the Thorite Decrees. Magnus the Red becomes the new Master of the Astronomican. The Age of Apostasy ends. The Age of Redemption begins: 515.M36-561.M36
-the Golden Throne requires an increase in psyker souls to maintain optimal levels, raising from one hundred to two hundred sacrificed each day: 789.M36
M37:
-the Astronomican flickers for several seconds, causing hundreds of voidships to be lost in the warp, and two thousand worlds across the Imperium to simmer with rebellion that would take decades to put down: 666.M37
M38:
-the Imperium's vast military might is exhausted and overextended after centuries of successful Crusades and Wars of Faith, allowing the secessionist Ultramarines and the Traitor Legions to reclaim the initiative, seeing to the capture of large swathes of Imperial territory. The Age of Waning begins: 213.M38
-the Fortress World of Cadia falls to the Black Legion and its allies: 783.M38
-several attempts are made to recapture Cadia due to its strategic importance but all fail, causing the High Lords of Terra to write it off as a permanent loss: 786.M38-799.M38
M41:
-the Iron Hands reveal themselves in significant numbers for the first time in millennia, invading the Gothic Sector and initiating the Gothic War: 139.M41
-The Iron Hands depart the Gothic Sector, having captured four of the six Blackstone Fortresses, the Imperium incorrectly declares the Gothic War a victory: 160.M41
-the traitor Iron Hands invade the world of Tanakreg, enslaving the local population. A Word Bearer relief force arrives, rallies the surviving Imperials and retake the planet, suffering heavy casualties among the mortals. The Iron Hands are defeated, not a single traitor legionnaire leaving the planet alive. The Tower of Blood is constructed to honor the Imperial fallen: 212.M41
-the Fourteenth Imperial-Ultramarine War begins with Ultramarine forces launching a daring assault on the Forge World of Calxios: 300.M41
-the Ultramarines are stopped at the world of Beravue, Imperial counter-attack retakes several dozen worlds but over two hundred will be integrated into Ultramar, putting the Realm of Hundred at just past 50,000 worlds. The Fourteenth Imperial-Ultramarine War ends: 331.M41
-the First War of Armageddon begins when a Space Wolf warband invades. The Khornate Marines are defeated by the combined efforts of the World Eaters and Thousand Sons: 444.M41
-the Sabbat Worlds are lost to Chaos forces led by Black Legion and Raven Guard warbands: 530s.M41
-the Goru Heresy begins, igniting civil war across three sectors. Elements of the Emperor's Children put down the Heresy: 650.M41-651.M41
-the Realm of Ultramar comes into contact with the Tau Empire. Due to ongoing border wars with the Imperium, the Ultramarines cannot spare the resources to invade: 698.M41
-after several costly border skirmishes, dubbed the Damocles Gulf War, a tentative peace is established between the Realm of Ultramar and the Tau Empire: 742.M41
-the world of Tyran is scrubbed of life, its atmosphere and biomass having mysteriously vanished. The Ultramarines investigate this phenomenon but come under sudden attack by a dangerous xenos species. This is the first recorded encounter of the Tyranids in the galaxy, this initial wave dubbed Hive Fleet Behemoth: 745.M41
-the Corinthian Crusade is launched by the Imperium, liberating dozens of worlds from the Ork empire of Charadon, stabilizing the border between the two states: 798.M41-807.M41
-the First Tyrannic War is waged throughout south-eastern Ultramar. The Ecclesiarchy calls this 'the Emperor's Judgment. The Tyranids attempt to invade Macragge but are only stopped due to the combined efforts of six Chapters. Though victorious, casualties are heavy: 745.M41-747.M41
-the Sabbat Worlds Crusade begins, the largest mobilization of Imperial forces in centuries, with nearly a quarter of Segmentum Pacificus dispatching forces: 755.M41
-the Sabbat Worlds Crusade ends in victory, but the Crusade left several sectors in Segmentum Pacificus vulnerable as their defenses had been stripped bare and are raided by Raven Guard forces: 783.M41
-Hive Fleet Gorgon attacks the Tau Empire and Ultramar, and though it is far smaller than Behemoth, it is more adaptable. Ultramarine and Tau forces fight together to end the threat, eventually securing victory: 899.M41-903.M41
-Hive Fleet Kraken invades the Imperium for the first time, ending the false religious rhetoric that they had been the 'Emperor's Judgment.' Kraken is defeated after immense cost to the Imperium: 900.M41-903.M41
-Black Templar Marshal Lufgt Huron brings the worlds of the Badab Sector back under Imperial control after centuries of independence. The Black Templars combat rebels, xenos and Chaos forces during the Badab War, defeating all. This campaign greatly increased Huron's reputation within the Sixteenth Legion, elevating him to the hallowed council of the Mournival: 901.M41-912.M41
-the Golden Throne now requires a thousand psyker sacrifices daily to maintain the Astronomican beacon, though it is rumoured to be dimming, causing hundreds of worlds on the outer edges of the galaxy to become lost: 916.M41
-the Second War of Armageddon occurs when Ork Warboss Ghazghkull Mag Uruk Thraka leads his Waaagh! to the Imperial world. Is defeated but he escapes to reform his army: 941.M41
-the Black Legion and Salamanders fight over the Imperial Cardinal World of Heletine. The resulting Promethean War saw a half-dozen star systems scoured of life, with some taken as slaves but most butchered by the two Chaos factions: 980.M41
-Hive Fleet Leviathan arrives, invading both Ultramar and the Imperium, forcing both sides to sacrifice whole worlds just to stem the tide: 997.M41
-Chapter Master Marneus Calgar begins to implement innovative technology in the Ultramarine Chapter and attempts to spread it to his fellow Chapters of Ultramar, experiencing little success: 998.M41
-the tech-priests of Mars inform the High Lords of Terra that the Golden Throne's mechanisms are beginning to fail and that they are unable to repair it: 999.M41
-the Tau Empire, sensing weakness in Ultramar's borders, invade, capturing a score of worlds before stopped. The Second Damocles Gulf War officially begins, neither side unable to gain the initiative: 999.M41
-the Third War of Armageddon begins, draining manpower desperately needed elsewhere: 999.M41
-the Cicatrix Maledictum forms, splitting the galaxy in two. The Chaos Legions, united under a single leader for the first time since the Dornian Heresy, launch the Chaos Black Crusade, commanded by the Champion of Chaos, the Inheritor of Dorn, Sigismund the Destroyer. Dozens of sectors within the Imperium Nihilis fall to the hordes of Chaos, with scores more under threat. The Ork empire of Charadon begins to rapidly expand, encouraging dozens of lesser Ork empires to follow suit, furthering putting a drain on already thinly stretched Imperial resources.
-a thousand rebellions erupt in Segmentum Pacificus, created by Chaos cults. Traitor Space Marines and their mortal slave-armies invade the Segmentum, conquering hundreds of worlds with ease and setting their sights on thousands more: 999.M41
-Fulgrim the Phoenician returns after ten thousands years, arriving to Chemos and reassuming command of the Third Legion: 999.M41
-the primarch secures a minor, yet crucial, victory on the Cardinal World of Scound's Fall in the Segmentum Solar. The Living Saint-Prophetess Amelia Jakoby joins his retinue and swears fealty to the primarch: 999.M41
-Fulgrim and two thousand Emperor's Children arrive to Terra. Fulgrim meets with the High Lords of Terra to decide the fate of the Imperium: 999.M41
* = The way Aurelius Rex wrote the DH made it seem like the Heresy lasted only a couple of months. Like Dorn and his allies traveled from Istvaan to Terra in a matter of days. And no other battles of the Heresy were mentioned aside from the Istvaan Dropsite Massacre and the Siege of Terra. For this war to be truly as devastating as it was, it needed to be several years long, so I went with the default seven.
** = The Age of the Imperium technically lasts from its founding with the union of Terra and Mars up to the current day but has multiple "sub-Ages" within it.
