There has always been an unseen war between Biblical and Evolution imagery in the Megaman games. In MHX, Sigma tells Vile that he wants to go maverick to speed along the Reploid evolution. When confronted by X as to why he is committing mass murder, he answers, "Evolution requires Sacrifice."
The MHX Sigma is very similar to Hitler who started the holocaust for many reasons but one in particular was that he considered them to be inferior beings. He thought the Germans were the superior race and he believed that He should remove the inferior race to speed along the German evolution. He might not have said those words specifically, but that is what he most likely believed. History tells us that Hitler sanctioned medical experiments on women and children to change their eye color to blue so he could have a superior race of blond-haired, blue-eyed people.
Sigma is little different. He was willing to cost the lives of millions of people to speed along his evolution. Although it is likely that this bears no major importance, as the series progressed Sigma placed a keen interest in Zero, who has blond hair and Blue eyes- two of the three to four things that Hitler considered to be the ingredients to a pure Aryan. It should also be noted that before Hitler came to power he was a copal in the German military. Sigma was the leader of the Maverick Hunters before rebelling to become the supreme ruler of the world.
Lumine was totally unscathed with the thought of killing off X, Zero, and Axl as well as all the first generation reploids in the name of evolution. He displayed great arrogance in his status as a new generation reploid as if the others were worthless animals. What is most interesting is that X had no way to morally combat Lumine's thinking, as the concept of creation-centered philosophy is foreign to him.
The quest for evolution inspired another rebellion in Command Mission and ended with the death of at least 22 people including many resistance fighters. Once again X could not think of a moral reason why Colonel Redips was wrong. By the time you reach the end of the x-series at least 3,001,002 (estimated casualties of the six wars and 3 uprisings of the x series) died in the name of evolution.
Dr. Weil, who hated reploids because of their rebellions, caused the elf wars, which in the end eliminated an estimated 15,134,109,125 (60 percent of humans and 90 percent of reploids) people. None of this would have happened if Sigma had not rebelled, and Sigma and others like him would not have rebelled if the concept of a creation-centered worldview were presented to them. At least 986 people were killed by the Serpent Company's mavericks in the name of evolution. It is worth noting that Satan's serpent form in the Garden of Eden was the form he used when he first introduced the concept of evolution to man (Ye shall be as gods Genesis Ch 3).
Each of the main players in Master Albert's Game of Destiny explored the different branches of the evolutionary viewpoint.
Thetis, the Ice Megaman, explores the evolution's environmental beliefs. He clearly values the Earth's oceans more than the Earth's people. He holds great contempt for the humans who have to desecrate the earth to live. He treats the earth as a living being and considers it more important than people. He actually preferred humans to be scarce in population. Coming from an evolutionist perspective, this is hardly illogical. An accident created the earth and since there is no creator guiding the cycle of life, it only stands to reason that another careless accident by man can destroy it. Thetis's worship of the earth is only natural considering his evolutionary beliefs. He is not the first to hold this belief either; the environmentalist agenda of today advocates the sacrifice of human efficiency and human life to save the earth from a threat that does not exist. Unfortunately too many people are blinded by environmental hysteria to see that despite all the years of bloodshed and mayhem, man has not come close to poisoning the earth's oceans. This fact has gone unnoticed and as a result Thetis became a mass murderer.
Atlas, the Flame Megaman, explores the social Darwinist side of the evolutionary worldview. The sole survivor of a maverick raid, Atlas has embraced the idea that might makes right. She deliberately causes bloodshed and mayhem just to get stronger and wipe out the weak. She has no sympathy for her victims because she decides that they are not innocent just ignorant of the fact that only the strongest deserves to live. In her mind, wars are necessary to flush out the weak so the strong can evolve. This is following Darwin to the letter who himself said "Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows."
Aeolus, the Wind Megaman, embodies the arrogant stance of an evolutionary 'fit' being. Where Atlas murdered beings that were physically weaker than she, Aeolus focused on eliminating the ignorant and the foolish. He reasoned that stupid people feared and therefore destroyed what they did not understand and therefore were the cause of conflict. While one can make a point with this logic, Aeolus himself was too foolish and ignorant to realize that he was hardly qualified to be the judge of all the earth. Aeolus believed that his intellect was great enough to be the intelligence standard based upon his own intellect. He is using a rubber ruler to measure intelligence. How can anyone declare themselves the smartest beings alive without getting trapped in the cycle of circular reasoning? Without the concept of a creator, intelligence cannot be properly measured. But because Aeolus is an evolutionist, he does not see this and ends up proving his own point: "stupid people" who kill things they don't understand, are causing many of the problems in this world. Thus the self proclaimed perfect Megaman has become the perfect hypocrite.
Sirnaq, the Shadow Megaman, is the personification of the paranoia that would permeate a world that has fully embraced the evolutionary philosophy. In such a world, utilitarianism would reign supreme. The second you were declared useless is the second you would be eliminated. This would be truly frightening considering that the definition of "useful" varies from person to person and with 6 billion people in the world to satisfy, you would be in quite a handful. Sirnaq experienced this first hand when he was beaten and left for dead by his own friends. This betrayal is still could still be seen in his speech patterns; he spoke in robotic monotone and gave as little information about himself, most likely to make sure that he was never betrayed again. It is interesting that he did not reveal any plans on the direction he would take the world. What this means is anyone's guess, but one could make the connection that in the paranoia of an evolutionary mindset, there is little to no room for helping others or the fact that evolution spells out no real purpose other than to stay alive.
Master Albert is the final piece of the evolutionary viewpoint: the desire to become God. Just as King Solomon wrote in Ecclesiastes, Master Albert concluded that the only thing that this world is good for is emptiness and misery. It was just an endless cycle of war and bloodshed. Though the reason for conflict may vary, it happens none the less. To fix this problem, he created Megamen to evolve. He declared himself the god of this world and decided to wipe it out to create new life. In a sense he embodies the evolution branches of the 4 megamen- The elimination of the weak (Atlas), the glorification of intellect (Aeolus), the protection of the new life/word's future (Thetis), and survival (Sirnaq).
It was all the more fitting for Albert to die on the Ouroborus Biometal as it was in the shape of a snake consuming itself in the same way Albert and those before him were doing in their quest for godhood. Sadly, the blood continued to spill because despite everything they went through, Grey, Ashe, Vent, and Aile continued to hold on to the idea that the world belongs to man.
Interestingly enough, it is not until the most peaceful period, the Legends series, do the carbon characters suggest that they were created rather than the result of evolution. This makes it very fitting that the period of peace is present when there is no evolutionary mindset to justify genocide. This is the only way you can have an absolute standard of morality, through a creation mindset that says right and wrong come from the creator.
The problem with an evolutionary mindset is that you end up with moral relativism or moral neutrality.
It is the intellectual equivalent of having construction workers build a house, but having them use different metric systems.
To one guy 1ft is 12 inches,
to another guy 1ft is 36 inches,
to the third guy 1ft is 5 inches.
If the owner of that house wants it to be 6 feet wide and 12 feet tall, with 10 windows 4 of them 3x5 feet, 5 of them 7x3 feet and one of them 4x5 feet, how is that house going to turn out if they all have their own standard?
With this moral dilemma among the populous shoveled, the only ones causing any major death are the Reaverbots and obsolete units such as Megaman Juno.
What is also interesting is that in almost every area the evolution is mentioned, there is often a Biblical reference near by.
For example: Dr. Cain 'killed' Abel City's population by creating reploids, the best of which, Sigma, who decided that evolution requires sacrifice.
In the Bible, Cain killed Abel (and in the process 1/4 of the population). Evolution is the basis of secular humanism, the most vocal critic of any and all Christian influence.
Another Example would be found in X8. Sigma once again uses evolution to justify his rebellion. Lumine also shared his philosophy which is why he orcistrated the events so that he could kill Sigma and take his place. He took it a step forward saying that only the New Generation Reploids deserve to live and all others be they reploid or human must die. Just as there is heavier emphasis on evolution, there are more Biblical references as well. Jakob's ladder is a Biblical reference to Man's desire to reach heaven.
Sigma's Belial form, in Milton's Paradise Lost, was a servant of Satan. Satan was the one who introduced the concept of evolution to man in Genesis ch 3. Having Sigma, who appears to be evolution personified, take the image of a servant to Satan, is all the more fitting as it was this concept that Satan has used throughout the history of mankind to convince people such as Adolph Hitler, Joseph Stalin, Leon Trotsky, and Pol Pot that there is nothing wrong with eliminating mass groups of people for the greater or good, or as Sigma puts it "Evolution's sacrifice." Having Lumine take the form of an angelic being is even more fitting as he is taking Sigma's ideas to the logical extension and he takes the form of "an angel of light" a disguise given to Satan by the apostle Paul. Finally, Jakob's ladder was constructed in the Galapagos Islands, the area where Darwin received his inspiration for his evolution theory.
A third example is seen in command mission where we have two main characters wanting evolution and two Biblical references. For the first time we see the mention of prayer by a reploid no less, and of course the Babel tower. What is interesting is that Redips had set up shop at the top of the tower of Babel and at the end, the pod they are on crashes into the earth and again the hunters are back to square one. This is an homage to the Humans in Genesis 11 where the humans want to "make a name for themselves" by staying unified and building a tower to the heavens. Since they would not scatter, God confused their languages and they were back to square one. In Redips' quest for evolution he only brought destruction of what was already built and in Man's quest for godhood, and the ability to do anything they wished to do, they brought nothing but disorder and chaos.
A fourth example is seen in ZXA. Evolutionary ideas permeated the story but none the less a big Biblical reference is seen: the Sage Trinity which is an obvious homage to the Holy Trinity.
In conclusion, we see an increase in Biblical and Evolution references in the games that seems to imply that in a funny sense the unseen war of religious 'spirits' is still going on behind the scenes of the games. It's like a shouting match in a soundproof room. You can't hear the cries but you can see the effects on the characters and the story.