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is The Emperor= Tony Sark

and Horus= Captain America

or the other way around?

Not even remotely comparable.

Settings are too different. Even in his goodguy phase, Horus was committing mass genocides without regret as were all the Primarchs. Even Vulkan executed a surrendering Eldar child.

isnt that still a xenos though? sad as is by our standards. but to them. it was and is an us or them mindset.

These really are not comparable situations. The actual stimuli that spurred on these civil wars are completely, hilariously different. The Horus Heresy was about one man being deceived into thinking his father had betrayed him, and him literally selling his soul and the souls of his brothers to a pantheon of demonic gods in order to bring judgement to his father for an imagined slight.

The Civil War in Marvel (at least in the comics, and I presume in the film) was about a conflict of ideologies spurred on by a tragedy (reckless superpowered teens causing the deaths of innocent civilians that included schoolchildren). This lead to a war between those who favored freedom over security and those who favored security over personal liberty.

There's a lot more moral grey in Marvel's Civil War than there was during the Horus Heresy. There's not a clear, defined "bad guy" in the Marvel Civil War (even though they like to push Iron Man as the villain). Sure, The Emperor was a dick, but there's no doubt that the side fighting for demonic abominations from another plane of existence are the bad guys in that story.