Why was "remove humanity" the end goal of all X villains?

Why was "remove humanity" the end goal of all X villains?
At least the main ones, Berkana just wanted more power.

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en.wikipedia.org/wiki/Polymorphic_code
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capcom-unity.com/devroom/blog/2011/04/15/kinakos_daily_report_72
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Race war.

Who?

Humanity was the ones controlling them. See the Matrix.

A decent number of Reploids think themselves superior to humans due to their superior physical capabilities coupled with human intelligence, though the Zero and ZX games make the point that Reploids didn't really get to human mental stability or physical dexterity in almost all cases until the Sigma Virus was wiped out. The ones that go too far with the "muh superiority" bent get branded Maverick as well as ones that go crazy from hardware/software failure. They're kinda like sci-fi jihadists.

Mega Man Xtreme 2 villain. Xtreme games were kind of a stripped-down Game Boy Color version of X1, X2 and X3 like the Mega Man games made by Minakuchi Engineering for Game Boy, and though they weren't really important they introduced a handful of custom villains of their own.

Do you want the long, detailed version or the short, boring version?

The long detailed version

Give me a bit.

Good question. Let's explore that further.

You'll probably know most of this, but you should probably read all of it in order to make sure you're not missing anything, because you need it all. I'm writing it as though you missed lots of important things, even though if you're asking this question, that's obviously not the case. Some of this is not expressly said in games, and there are some conflicting stories from official sources, but this is the best possible explanation as I've come to know it.

tl;dr at the bottom.

First thing worth knowing: X and Zero's designs contain something along the lines of DNA. Everything is based on that.

So basically, X, being the first robot (intentionally) built with a true free will, contains hardware (and related software) that gives him a sense of humanity, like humans have, rather than leaving him as a complete sociopath, which would be the expected default. This hardware makes him not insane, and leads him to question everything about himself, his motives, and whether or not he can be considered to be doing some kind of "good" based on his own experiences, in a way roughly equivalent to a person. This hardware was imperfect, though, and leads to excessive questioning. The severe battery of testing that X underwent while sealed in his capsule was necessary to lead to the desired result, which succeeded, but in addition, X was left in a perpetual state of "Why?"

On top of this, when Dr. Cain discovered him, and tried to make replicas of him, these systems were not fully understood, and the resulting robots, (reploids) either do not have the same systems within them, or do, but have a malfunctioning counterfeit of an already malfunctioning genuine article. As such, they're not as stable as X, and, while the chance is fairly low, there's an extremely remote chance that they can spontaneously become insane, sociopaths, or otherwise destructive. This same gimped system found its way into Sigma.

Zero was never properly completed by Wily. Wily somehow understood the principles of creating a truly free-willed robot, presumably from his time working on Proto Man, well enough that he decided to begin work on one to leave one as his ultimate legacy, believing that he could finish it. However, there was a flaw with Zero's programming that made him exceedingly violent, even when there was no reason to be. Wily was never able to figure out what caused this flaw, and died while working on him, leaving Zero in an incomplete state, and in permanent stasis in a hidden laboratory, much like X.

Wily's other pet project was the Zero Virus, which was a success. The Zero Virus is a polymorphic virus which infects computers, but mainly robots, and causes them to behave erratically, and usually violently, generally causing disarray. It can also be transmitted wirelessly, whether the target robot is specifically listening for it or not, and by direct touch. Like most viruses, it's possible to be a carrier for it without showing any symptoms, and symptoms can arise later on, despite not showing previously. There's no known way to counter it, and it seems to adapt to measures taken against it. As a practical weapon, it's fairly useless, as it cannot be directed. However, the real use of the virus is that it contains the mind of Dr. Wily, who somehow successfully digitized himself. Simply by existing, Zero produces and spreads this virus. In this sense, Zero is essentially Wily's robotic phylactery. Without going into exactly how it works, or what the end-game is for it, Wily has succeeded in becoming a techno-lich.

en.wikipedia.org/wiki/Polymorphic_code
techopedia.com/definition/4055/polymorphic-virus
That probably leaves a lot of questions open, and it's because there's a lot more to the purpose of the virus than this, (at least a few more paragraphs,) but it's not especially relevant to your question. I'll go into it if asked, but I'm focusing on answering as succinctly as possible. (Mid-script Post Script: I lied.)

The virus has been shown to modify itself based on the robots which it infects. Most notably, the first robot other than Zero to be infected, Sigma.

Before the events of the X games, reploids had only existed for a few decades, but it rapidly became clear that Mavericks, at this point only occasionally caused by the extremely minute chance of malfunction, would pose a threat, and thus, the Maverick Hunters were created, which X would also later join. Sigma was was the most advanced reploid in history at that point, and was created with the most sophisticated systems available, rivaling those of X, including logistics systems specifically designed to be capable of handling any strategic combat scenario on any field of battle. It was for this reason that he was given command of the Maverick Hunters. However, he still possessed the failed counterfeit copy of the empathy hardware within X.

Sometime later, still before the events of the games, a team of Maverick Hunters was exploring an abandoned facility, and discovered Zero. They awoke him, presumably by accident, and he resumed his programming. Zero outclassed every reploid that existed at this point, with the theoretical exception of Sigma, and overwhelmed, they called for Sigma. During this fight, Zero nearly defeated Sigma, but was forcibly stopped by something which caused him great pain, implicitly directly and intentionally by Dr. Wily. This allowed Sigma to land a surprise punch directly to Zero's main power crystal, shattering it. This is the point at which the "Remove Humanity" meme was created. Sigma ordered for Zero to be taken back to Hunter headquarters for study.