The lost leigions
1. The lost legions and their Primarchs are the Alpha Leigion and it's twin Primarchs Alpharius and Omegron, and possibly remnants of another leigion, either meaning there's only one missing Primarch or the Alpha Leigion has 3 Primarchs and is in-fact the scale of 3 leigions (explaining the three headed hydra and the fact even post-heresy the leigion seems larger than should be possible)(or the two replaced one unnamed Primarch was actually lost, perhaps returning later as "the false Primarch")
2. Malachor and the Emperor are not Malachor and the Emperor and a Successful coup already took place prior to the Horus Heresy the victors altering the memories of the other primarchs, etc. creating the legend of the Lost Leigions (and explaining why all imagery of the "Lost Primarchs" was eradicated while the same was not done for other traitors. A pact with Chaos likely playing some part in the subsequent deception, (e.g. the utter inconsistency of the Emperor's powers, able to personally lay waste to entire continents with force equivalent to multiple imperator titans, but only in the heat of battle and only while planet-wide slaughter takes place in his name (pact with khorn?), imperial 'thunder-bird' icon used by the emperor since ancient times replaced by the two headed eagle obviously resembling a 'changer of ways' (pact with Tzench). (laws protecting mass perversions committed by members of the Navigator houses, usually ending in the horrific murder of the victims, thus imitating the behaviour of the corrupt pre-fall Eldar (ritual for Slanesh)(deliberate general stagnation, disease and poor conditions on imperial worlds (ritual for Chaos God Nurgle?)
The Emperor's mastery of technology and power to reshape it with a touch is dubiously similar to the abilities possessed by the Martian 'Cult of the Dragon' and in the emperor's case seem conspicuously lacking in instances he is away from Mars (can completely fix a Tempestus knight with a touch but can't remove or deactivate butcher's needles (something that 'the cult of the micro omnissia', or a 'magos biologos' and even 'lexi-mechanic' of Adapus mechanicus should have been capable of)
A. Malachor and The Emperor are actually primarchs 2 and 11
or
B. just the Emperor was replaced and the dethroned Emperor is drained and made to believe he is Malachor (malachor has more consistent but "weaker" powers than "the Emperor", his offspring seem to have vastly greater outright psychic power then the emperor's descendants (sacrificing a single member is said to have the energy to awaken the "Star-Child" an act which would allegedly otherwise require almost all the emperor's surviving descendents), and he wields a weapon resembling the burning Staff from the prophecy of The Omnissia (a prophecy allegedly secretly written by the emperor))
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3. Jonus Milas and his bound Psychers became Perpetuals or even became some of the ruinous powers when they are killed by the akashic reader (Jonas himself potentially becoming Tzench)
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4. The Necrontyr went on to become not just the Necrons, but through Qua's secretive intervention also became the Hrud and eventually after migrating backwards through time were 'completed' by a younger Qua and also became an earlier version of the Eldar, and later another off-shoot of the necrontyr race eventually becoming the Tau
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5. Zoats are a Psychically parasitic species that subsumes themselves into other societies as workers, slaves, advisors, guards, etc. and proceed to "rule from the bottom", psychically conditioning their unwitting and apparently dominant host species into a state of dependency and vulnerability. (Early less adapted Tyranid variants cooperated with and fought alongside Zoats , many Eldar had Zoat advisors and the Zoats claimed they wished to serve the Imperiam to help them defeat the Tyranids, (in this case, being immediately exterminated by the imperium instead, strange that the all consuming tyranids hadn't eradicated them and even "chose" to make up half it's forces from their number, as soon as the Zoats were removed however the tyranids themselves soon became rapidly more formidable foes and the Zoat-Like "Dominators" leading their armies were soon replaced by synapse creatures)
6. The Old-One's "Degenerate descendants" who the C'tan liked to hunt may actually represent a sub-race of malignant Old-Ones (effectively Chaotic Old-Ones)
7. The Necrontyr became Old-Ones when they died and so a malign faction of Old-Ones cursed them with their rapid degradation to speed up the process, also being the reason the Old-Ones refused to grant them longer lives, ('they would be dead soon enough so why spoil the surprise that very soon they would be reborn in the imarerium and live forever'), this is also why the Ctan tricked the Necrontyr into undergoing bio-transference and why the Old-Ones couldn't effectively replenish their own numbers during the war with the now Necrons
8. Some C'tan aren't "C'tan": heavy celestial objects are often places were the Warp and Real-space exert greater influence on one-another as even the Old-Ones and possibly even the C'tan themselves didn't seem to fully understand what the necrontyr had done when embodying C'tan using the Starlight-Bridge to place them in necrodermis bodies, it stands to reason that the Necrontyr didn't either, and since aspects of The C'tan's knowledge came from the stored historic repository of the Necrontyr race, then upon awakening it would have little reason to question it's first knowledge of the world e.g. that it is a member of the C'tan, this would explain why they are apparently so valuable to the warp, the ones who are warp entities are simply pulled back to the warp on contact (the Outsider literally radiating insanity and being the one and possibly only C'tan who was "physically wounded by consuming other C'tan" and also the one C'tan who is known for feeling shame or guilt)
9. many ret-cons in wh40k lore are the result of Orikon the Diviner attempting to make his 'inaccurate' prophesies seem true and endlessly confounding the original paradox caused by one of the first changes, the unseen opponent he struggles against throughout time being past and future iterations of himself as he unintentionally invalidates his own prophesies causing his subsequent and earlier self's to do the same, causing endless rippling fractures in the timeline, multiple much later iterations of himself trying endlessly to restore what for them seems to be the original timeline, The Mysterious Necron sphere traveling the universe rewriting each planet's history being one such attempt, The Brotherhood of sentient races who tried to change the outcome of the Horus Heresy, and where noted as having at least one member who was Mechanical, being another
10. The Enslavers are far more closely related to the Old-Ones then they appear to be (noting their occasional vague similarity in physical appearance to certain entities appearing in H.P. Lovecraft's works, (aspects of which also allegedly inspired the design of the C'tan backstory for the Necrons , who's war with the old ones causes the Enslaver Plague to be unleashed) (or maybe they're the Equivalent of Qua's Umbra for another defeated but perhaps more malignant Old-One)
11. Slanesh was originally meant to be a benevolent Slan deity to stabilise the warp, but the 'Fall' Eldar's depravity and corruption ruined it when the partially formed 'god' was flooded with the endless torrent of veng, screaming souls of the Eldar's defiled victims, Slanesh's first acts after being born were effectively to punish the Eldar for their vile actions, to Devour their gods for their inaction and to shatter Qua turning him into the Umbra race as a punishment for lingering in the warp and not taking action to right the wrongs of the universe, saying something along the lines of "Since you lingered here and did nothing, linger forever" (when an Umbra dies it also emits a psionic scream consisting of the word "Linger" shouted in a million voices)
12. The Chaos god Nurgle was originally a benevolent god of the Old-Ones, representing a life bringing fatherly figure, (and why he still represents a caring grandfatherly figure to many of the younger races who serve him), when the immaterium was tainted and the eldar / necrons / old-ones / C'tan had decimated life in the universe with their war he also became the Chaos god of death, decay, disease and plagues, it is likely why he sympathised with the eldar goddess isha (the goddess of life and healing) this may also relate to the fact some of his darmons are imune to the pull of the warp and can reproduce in the "real-world" without needing a significant connection to the warp, they may infant be fully functional accurately crafted life-forms rather than just manifestations of his will
13. Chaos Tyranids ( genestealer cults are sometimes dedicated to Chaos powers, forming Genestealer Coverns and at least one hive ship was at some point modified by Nurgle to suit his personal preferences and later returned to 'real space' )
14. 'Chaos Necrons' may have been created during the events in the early necron codex when a vast disfigured sphere of insanity inducing necrodermis found on a spacehulk is deliberately pumped full of warp energy from the ship's engines on the orders of an inquisitor, the object is last seen becoming a black monolithic shape before contact is seemingly lost and the ship is seemingly destroyed
15. The emperor's golden throne was originally a 'more advanced' akashic reader used for creating "men of gold" during the dark age of technology
16. the emperor is Belakor (or belakor was made from fragments of the emperor collected when he made his bargain with the chaos gods, (similar to the ones they each kept from Horus Lupercal)(both are shape shifters, belakor is known for raising empires and deliberately leading them to stagnation or destruction)(and a stone map in the ruins of an alien civilisation depicted earth from the the time of emperor's youth
17. the Motive-Force, Machine-God, Omnissia trinity of the adeptus mechanicus is infact The Void C'Tan Dragon, The eldar God Vaul, and a human vessel of knowledge, initially the 'young' Belesarous Crawl before his mind was wiped during the age of strife, (the noctics labyrinth being a physical nexus of the ~three entities Vaul imprisioned high in the labrynth, The Void Dragon imprisioned at the bottom and the area in between being a shifting space representing a contorted overlapping representation their minds, which joins or resonates with the mind of each potential omnissia, (note the 'modern day' Crawl has a mostly mechanical body which contains a mesh of souls and has entities at his command which could be considered physical mechanical equivalents of a Warp god's lesser Daemons, or of a C'tan's shards, e.g. the sub-Crawls that populate his ship (implying he is gradually becoming a 'real world' analog to the worshipped Machine god, the fact all three aspects of the god are existing entities and imprisoned by or bound to the service of, the Imperium likely explains why the warp seemingly hasn't yet birthed a new machine deity to represent it)
18. At least some of The Leigion of the Damned are also the Thousand Suns impersonating the Firehawks (e.g. re-manifestations of some of the Thousand Sons who were turned to dust)
