First, I would like to give some context to these two questions. I am relatively new to the WH40K universe (but I played Space Crusade 20 years ago! Ahem ). I actually like the universe in itself: I like this dark world where really, the "good guys" would be considered pretty bad by anyone else's standards nowadays. I really like the Chaos Gods, what they stand for, and how they act as forces of nature, etc. I truly do. I've read a few novels too (the Grey Knights trilogy and am finishing the Eisenhorn trilogy as we speak). In other words, I have taken a real liking to the whole WH40K universe, even though I am not much into the figurine part of the game. I do not currently play with anyone, but I acquired Rogue Traders, Only War, and Black Crusade. I am currently reading through BC, which I find extremely interesting on its own.
In addition, I am not new to role playing and in particular with playing "adult-themed" RPGs. I've played nice and less-than-nice or even nice-turned-monstrous guys in the context of Vampire: the Mascarade games (and in particular, I've been a story teller in a small campaign for a Sabbat pack), I've been a "white collar" slave master in games of Kult, etc. In other words, I am not a stranger to playing games with ambiguous themes which involve people with less than pristine minds. Yet, I find it hard to see how to use BC on its own, without a "wider scope" where other WH40K games possibly intervene later in the story.
What follows may seem off-topic, but please bear with me, there is a reason I dedicate a full paragraph to a game that is not BC.
To go back to the Vampire/Sabbat example: sure, in-game, the Sabbat is a violent sect, which strives to set itself on top of the proverbial Darwinian only-the-fittest-survive food chain. Yet, a vampire must obey whatever "moral" Path s/he has chosen to undertake, lest the beast inside takes over. Moreover, while the vampires of the Camarilla (which is the default setting used by most GMs) believe the older, powerful demi-godish Antedeluvian vampires to be legends, the Sabbat exists specifically because they believe in their existence, and think they're going to be snacks for them when they decide to awaken. And so they want to take the battle to them, by any means necessary. They believe in a quasi-fascistic way of ruling themselves, with a fanatical dedication that is terrifying. Yet, they do so because they believe their very survival depends on it. Are they considering regular humans as cattle? Sure! (and the fact that they used to be one of them is of no consequence). Are the Paths followed by Sabbat vampires leading them further and further away from their former human selves? Definitely. Are they right in believing that the legendary Antediluvian vampires are out there to eat them? Well, it depends on your GM, but if you read the material written by the game designers, it seems that while their methods of operations are extreme, they are justified in their beliefs at the very least.
Back to Black Crusade. The way I see it (and note that I have not yet read any Horus Heresy novel, nor have I read any Codex — truthfully I want to read a bit more of the 41M novels first before I read the former, while I don't intend to read anything from the latter), the Imperium of Man is already a very dark place to be, and in many ways "evil:" psykers are either exterminated or forcefully indoctrinated to become tools to navigate among the stars, or maybe become inquisitor material (or space marines). It looks like some people are "grown" just so that their organs can be collected and help created "intelligent" machines to better serve the Imperium. From a 2nd Millennium point of view, this is utterly terrifying, especially when one learns later what happens to people who openly criticize the cult of the Emperor-God, and how easy it is to be labeled a heretic. Yet, at the same time, whether they are right to have built their empire like this or not, they do have a true foe to defeat: the forces of Chaos and their Chaos Gods. They are a corrupting influence on all of Mankind, and no means are too strict to get rid of the corruption they bring to the Imperium.
In that respect, it looks to me that the Imperium in WH40K is very close in many ways to the Sabbat vampire sect of V:TM. While you may find their methods extreme, and utterly despicable, you can understand where they come from: after all, there is a Big Bad Wolf lurking in the dark. Its fur is permanently reddened with the blood it bathed in, and it wants more.
Yet, BC is about playing characters which despise the Imperium of Man so much that they would rather worship Chaos Gods than serve the Corpse-Emperor one more second. I can understand why one would stand up against the Imperium: it basically crushes whatever and whoever does not get out of the way fast enough, killing innocents (directly through bombings, etc., or indirectly by grinding them through the system's cog). I can see how a PC could end up being bitter and jaded and want nothing with the Imperium. I can understand how a PC could want the death of an inquisitor, e.g., because his son was a psyker and was taken away by the Black Ships, never to be seen again. I can even understand how that could lead a character to be seduced by the power of Chaos.
What I can't understand, is how this would make a good and enjoyable experience to play as a PC on its own. I can perfectly imagine an ambitious multi-WH40K campaign where the players start as heretics and achieve something of significance (release a daemon lord, find a terrible Chaos artifact and use it to corrupt people and start new cults for Tzeentch, spill the blood of countless people, etc.), and then switch to another game, e.g., Rogue Traders, where the players come to get said artifact (not knowing what it is), and somehow end up being paid to smuggle it (while being told this is "just" a xenos artifact). I can imagine how they end up realizing what their cargo is, and they must make a choice as to how they want to deal with it. And then, why not have a final mini-campaign using the Dark Heresy game where the players end up confronting their own previous characters. I can see all that.
But I have a really hard time imagining a campaign solely based on BC. Can someone help me understand?
Thanks!