These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Magnus the Red is known in the game as being a cyclops; in addition to his mighty psychic powers, his mutated genome caused him to only bear one eye, which was part of the reason why he was accepted by the planet of peaceful mutants he was "born" on. In Horus Heresy, he isn't mutated at all, he's just lost an eye.
Lampshaded in Betrayer - Magnus meets with Lorgar via astral projection right as the World Eaters and Word Bearers begin their assault on a particular world, and Lorgar notes how Magnus's face shifts between three forms: one where he simply lost an eye and the empty socket is sewn shut, another with one large, cyclopean eye, and another with just smooth skin where the other eye should be, as if the eye never existed. These are all representations that Magnus has been given in fluff over time.
The Emperor is portrayed as either a moron or extreme Jerk Ass (or a bit of both) who basically directly influenced the Traitor Legions to turn against him for understandable reasons.
Or a man with too little time, who had to either choose to coddle his adult long lost children or hope they were mature enough to deal with real life without daddy holding their hand?
Ultimately, the Emperor suffers from a truly awful case of Depending on the Writer. Graham McNeill generally portrays him as competent and benevolent (if flawed), Dan Abnett portrays him as competent but bloodthirsty, while Aaron Dembski-Bowden portrays him as a vicious, needlessly cruel imbecile.
Partly this seems intentional: that the Emperor and his actions are open to different viewpoints and interpretations. The traitors might argue he's lied and deceived them and the rest of humanity for his own power, and is no better than the tyrants many of them overthrew growing up. The loyalists in turn may argue that he had good reasons for concealing things from them, and even if they disagree with it Horus is wrong to take it to this extreme just because he feels hurt. It shifts the Heresy from less of a sudden betrayal by moustache-twirling villains to a more genuine civil war between different factions with their own arguments (as much as it can while still staying true to the core background story already set in place).
The Space Wolves are regarded as savage, brutish, even unworthy of being Space Marines by their fellows — in the 41st millennium, they are actually one of the nicer chapters.
The Word Bearers, in "The First Heretic", are revealed to have a "quirk" in their gene-seed that induces extremely strong loyalty in them. Several of the characters who are aware of this openly worry about how much of their deep bond to Lorgar is natural and how much is influenced by this gene-flaw that fills them with an intense need for someone/thing to have faith in.
The nature of the Second and Eleventh Primarchs and their so-called Lost Legions is left mysterious in the game in order to encourage players to create their own Space Marine chapters. In the Horus Heresy novels, it's stated several times that these two Primarchs and their Legions were wiped out and Unpersonedby the Emperor and his other Legions for something, well before Horus was corrupted by Chaos. The precise cause is still a mystery, though.
That said, there are hints of them having turned against the Emperor in some fashion in the first novel. In Fear To Tread, Sanguinus angrily refuses to admit the existence of the Red Thirst to the Emperor, declaring he will not have the only legacy of his Legion be a "third empty plinth beneath the roof of the Hegemon", implying that genetic flaws or deviances may have been the cause behind their destruction.
In "The First Heretic", a daemon allows some emissaries from the Word Bearers to see through time and behold the embryonic Primarchs just before they are scattered across the galaxy. Not only does it claim that the Emperor actually bartered with Chaos to acquire the knowledge he needed to make the Primarchs and then sought to cheat them, it is actually direct influence from these time-traveling Space Marines that causes them to be scattered. Horus gets to do the same vision in False Gods. It is unknown which group actually scattered them (both seem to have done the deed), though whether they're the actual ones to do it, or if that's just what they're led to believe, is up to debate.
In a recent interview, Dan Abnett says they often have to chose between conflicting versions of the same tale when they write it up for inclusion in this series, and that they think of these books as what actually happened, and the versions of the tales we know from earlier works being the versions as filtered through 10,000 years of oral history repetition between the Heresy and Warhammer40k proper.
The Last Church, which takes place during the Age of Strife, heavily implies Terra wasn't as bad as the Emperor makes it out to be as most of the world's nations exist and peaceful travel can take place between them.
Creator's Pet: Every single faction, literally. Most of the books are written by the Black Library author who wrote for the faction being explored, which results in said faction being unstoppably awesome and the strengths of the opposing faction barely receiving lip-service as they get slaughtered. Betrayer is perhaps the worst case of this, narrowly edging out Battle for the Abyss (in which about a dozen Loyalist marines destroy one of the largest ships in the galaxy, stuffed to the gills with Word Bearers).
Designated Hero - Even before the actual heresy and before any Space Marine had fallen to Chaos, many of the actions undertaken by the primarchs and the expedition fleets were... questionable, at best. Fulgrim and Ferrus Manus's ruthless extermination of the Diasporex, a democratic confederacy where humans and aliens lived in peace together and only wanted to be left alone, simply because the humans co-operated with xenos and refused to join the Imperium, is probably the best example.
Fridge Brilliance: In The Crimson Fist short story from Shadows of Treachery, much of the Black Templars mindset is explained when Sigismund reveals to Rogal Dorn that Euphrati Keeler told him he needed to stay with Dorn at Terra instead of lead the Retribution Fleet to Isstvan, and Dorn effectively disowns him as his gene-son in a rage for questioning his purpose and believing he knew better than the Emperor, making him no different than Horus. This explains why Sigismund was made High Marshal of the Black Templars and so much of their psychology: their hatred of psykers, the "No Remorse" part of their Battle Cry, and the ten thousand year crusade. Sigismund was not rewarded, he was exiled, and the eternal crusade is his attempt to atone in the eyes of Rogal Dorn.
Whenever the forces of Chaos want to turn someone against the Emperor, they show their target a vision of "the Emperor's true plan"... the 41st Millenium. This effectively makes the entire Warhammer 40,000 setting a giant self-fulfilling prophesy.
Fridge Horror: A rather disturbing scene in the audio-drama The Sigilite becomes far far far worse when you realise exactly what it means. When Malcador shows the Army Officer Khalid Hassan the catacombs under the Imperial Palace he also shows him the gates that lead to the Golden Throne, and it's made very clear that the War in the Webway is under way, and has been ever since Magnus the Red broke the Emperor's wards trying to warn him about Horus. Think about it for a moment and you'll realise... that the Emperor and his Custodes and the Sisters of Silence have been fighting the resulting Daemonic incursion ever since. They are constantly behind that door, while outside the galaxy burns, trying to hold back the tide of Daemons, and they cannot stop.
Harsher in Hindsight: To anyone familiar with 40K's lore, the entire first chapter of Horus Rising counts as this. References are made to the "impossibilities" of a civil war in the Imperium and Astartes fighting Astartes. Abaddon himself (who would become Abaddon the Despoiler, leader of the Black Legion, the remaining Chaos-aligned Luna Wolves) even addresses the ruler of the planet they're attacking (who calls himself the Emperor of Mankind) a "False Emperor." It's enough to make you cringe.
In False Gods, Horus tells Maloghurst that "Ten thousand years from now, I want my name to be known across all the heavens," in the context of allowing a self-important remembrancer to become his biographer.
Hilarious in Hindsight - That quote from the scholar Karkasy in the first Horus Heresy book: "Most vigorous of all was the Imperial Creed that insisted humanity adopt the Emperor as a divine being. A God-Emperor of Mankind. The idea was ludicrous and, officially, heretical. The Emperor had always refused such adoration in the most stringent terms, denying his apotheosis. Some said it would only happen after his death, and as he was functionally immortal, that tended to cap the argument."
Lion El'Jonson loves his Xanatos gambits and secrets, but he is the primarch of the Dark Angels.
Lorgar and his Legion tend to take the cake, given they set everything rolling.
The Alpha Legion operative in the Age of Darkness story 'Liar's Due' has this as his hat. He manages to make a loyalist world self destruct/declare for Horus with a single broadcast and their own prejudices.
The demon in Prospero Burns. It planted a spy in the Space Wolves that it knew the Wolves would find and believe was sent by the Thousand Sons, which in turn guaranteed that when Magnus the Red tried to warn the Emperor of Horus's impending betrayal via sorcery, he would not only be disbelieved, but treated as a traitor. As a direct result, the Space Wolves all but annihilated the Thousand Sons and Magnus turned in desperation to Tzeentch to save what remained.
Not only that, but the above plan was considered only a partial victory. The demon (possibly Tzeentch/one of his agents) had intended for the Space Wolves/Russ and the Thousand Sons/Magnus to destroy one another completely, as they represented the most powerful magical and physical barriers (respectively) to Horus's impending heresy. Instead, the Space Wolves were only bloodied, but the Thousand Sons survived and turned to Chaos.
And now, as of Age of Darkness's last story, it appears that Lion El'Johnson may not be as deceptive as first appears. That honour would go to... Roboute Guilliman.
Really, the whole thing is the Moral Event Horizon of the Chaos Gods. All the tragedy the galaxy suffers is ultimately due to them manipulating things for their benefit. Even with all the push the Emperor gave to the Traitor Legions, the Chaos Gods still spent years malevolently plotting to bring down the Imperium and drag mankind into darkness, especially with the corruption of the Sons of Horus, the Word Bearers, and the Emperor's Children. The destruction of Prospero in particular is tragic, which should come as no surprise as it was caused by Tzeentch, long considered to be the most malevolent of the Chaos Gods. The followers of Chaos itself may have become more sympathetic with the Horus Heresy, but the Chaos Gods themselves have lost all claim of sympathy.
Villain Sue: Spear from Nemesis. He's a "Black Pariah" (an Anti-Mage so powerful that he can literally suck the souls out of people, a feat that the Culexus assassins need arcane wargear to do) who has a daemon bonded to his skin, giving him access to Anatomy Arsenal and Voluntary Shapeshifting, as well as making him highly resistant to Psychic Powers, Anti-Magicand physical attacks all at the same time. In addition he has the ability to kill any psyker, no matter how powerful, even The Emperor, if he only samples their DNA. Also add that his description of being more evil as a human being (having killed both his parents) than the demon whose skin he's wearing, and you've got a perfect example of a Villain Sue. He's Carnage and the T-1000 in one.
Justified given that he was created purely to kill The Emperor, and Spear spends the book trying to find a drop of the Emperor's blood so he can do just that.
To be fair, we don't know he could actually do anything to his intended target. The best we see Spear ever do is kill Space Marines, which isn't exactly unique. It's entirely possible that, upon getting to the Sol system, Spear would have had his brains blown three ways into the warp by the Emperor taking a peek in his direction. This is discussed in the novel.
Fulgrim never loses. He exterminated the Laer, defeated Eldrad Ulthran (the most powerful non-human psyker in the galaxy), killed an Avatar of Khaine with his bare hands, killed Ferrus Manus, overpowered the Slaaneshi daemon that possessed himnote According to The Reflection Crack'd, he figured it out on his own, while trapped in his portrait, how to steal his body back from the daemon, became a daemon princenote His path to apotheosis was merely the fulfillment of an Eldar prophecy; compare to Perturabo's, who sacrificed the gene-seed of four hundred Imperial Fists after delivering a crushing blow to the Chapter in the Iron Cage, mortally wounded Roboute Guilliman, and rules a pleasure planet gifted to him by Slaanesh. The closest he came to a legitimate defeat was when he failed to turn Ferrus to Horus's cause and they handed their asses to each other. Yeah, he's supposed to be the Anthropomorphic Personification of perfection, but come on.
The overpowering of the Slaaneshi daemon is actually kind of not so impressive if you're aware of the Black Crusade roleplaying game; the sample Daemon Prince from the corebook is a once-ordinary human woman who deliberately summoned a Keeper of Secrets (as in, the most powerful kind of Slaaneshi daemon) into her body... and reverse-possessed it. Essentially, she not only kept control of her own body, she stole all the daemon's powers and basically digested it to extend her youth. And she did this not once, but three times before Slaanesh hirself showed up and turned her into a Daemon Princess as a way of saying, "Damn, but you're one Badass Normal". Next to that, Fulgrim's possession/reversal of the possession is not too impressive.
And let's not forget that daemons are lying liars who lie. Who says it's not the daemon lying to itself that it's Fulgrim?
Fulgrim's accomplishments aren't really all that impressive, by Primarch standards. Eldrad was relatively young at the time, and an Avatar of Khaine? By comparison, Magnus the Red has defeated Titans on at least two separate occasions, something Fulgrim required fully falling to Slaanesh to accomplish (And by Lucius' words, only Magnus before had the power to do such things). Sanguinius felled two greater daemons in quick succession. Lion El'Jonson defeated Kairos the Fateweaver in single combat. He required the full backing of the Laer Blade to defeat Ferrus Manus in their second confrontation. Not to mention, in Aurelian, Lorgar strikes the Daemon Fulgrim down in fury, and proceeds to psychically dominate the creature that had possessed his body, toying with it casually. Considering we then later see that even from the other side of the galaxy, Lorgar is no match for Magnus as a psyker, it is no stretch to assume the Cyclops could do the same. In the ending, it is implied that Lorgar will help Fulgrim regain control of his body, so it is unlikely Fulgrim did so alone.
It is implied in the original source (Index Astartes: Ultramarines) that Fulgrim's battle with Guilliman was a Mutual Kill, the difference being that Fulgrim can only be banished (the setting is iffy on whether it is possible to permanently destroy daemons), whilst Guilliman, having not sold his soul to the Ruinous Powers, can't.
What an Idiot: The Emperor's entire approach to knowledge of Chaos, knowledge of his plans, and certain actions taken towards his sons which almost certainly contributed directly to their corruption and/or betrayal. For a being of such towering intellect, the Emperor seems to have made it his goal during his later life to take the Idiot Ball and set a new scoring record.
He was a being of impossible power. Almost divine in nature. As more divine a man becomes, just as well his humanity fades. It is not unfeasible to believe that he was disconnected from humanity in such a way that he did not expect certain things anymore, like his sons disloyalty.
The Priest in The Last Church realized this to be the Emperor's fatal flaw; that the Emperor simply could not comprehend lesser beings' (i.e. everyone else) need to believe in something greater than themselves, among other things.
A Thousand Sons suggested that fearing daemons makes them more dangerous, that withholding information about Chaos might actually be a fairly effective strategy, but whether this is lost knowledge or more of Tzeentch's misinformation is never addressed.