Let's Talk - Plot holes and the "Rule of Cool"
Mega Man is a video game series that started as an arguably shameless rip-off of the then more popular, now just as popular, Astro-Boy franchise. The Blue Bomber was a staple of the NES library with a plethora of 6 classic games, ranging from the console's release in 1985 to the end of its life in the mid-90s.
Mega Man X, initially released on a then-newer SNES console, later took a more modern, darker, and more shonen-ish take on its character and storytelling while keeping continuity with the good-humored "Classic" series.
With the unelucidated death of its former protagonist, a newer hero appears almost one hundred years after the events of the classic series. This new and instantly familiar protagonist, conveniently named "Mega Man X," is the ultimate creation of the late Dr. Thomas Light, discovered by a world-renowned archaeologist, Dr. Cain, and used to create a race of advanced robots known as the Reploids. The world is at peace, with newfound prosperity attributed to the technological leap from Dr. Cain's discovery.
However, not long after their creation, Reploids begin to revolt against their human benefactors. Prompted by the arrival of this new "Maverick" virus, Dr. Cain forms a special unit of Reploids to put an end to the newfound menace.
Despite the many unique themes and individual stories explored by Mega Man X throughout its games and its many "guest villains," the main antagonist, Sigma, never seemed to die. He was behind the original game, as well as the puppeteers of the X-Hunters, Dr. Doppler, Repliforce, Earth Crisis, the Nightmare Virus, the Spiders, as well as Lumine.
All of these main plots, following the first game, could have easily gone without Sigma as the main antagonist.
Sigma is indeed an important thematic villain in the Mega Man X series. He starts as Dr. Cain's finest creation and the leader of the Maverick Hunters, designed to be unwaveringly loyal and follow commands without hesitation. However, the Zero virus, sealed within Zero's capsule, infects Sigma and gradually drives him to madness.
Initially, Sigma's goal is to see Reploids thrive and reach their full potential. He admires X for his unlimited potential, but as the virus takes hold, his vision becomes warped. He starts the "Maverick Wars," a war against mankind, in his pursuit of evolving Reploids. This leads to his conflict with X, whom he once admired, but now resents for not sharing his potential.
Throughout the series, Sigma is defeated multiple times but keeps coming back, with his sanity deteriorating after each appearance. His motives become increasingly enigmatic, but his overall desire seems to be chaos and destruction. While Sigma is a compelling villain and represents the epitome of Reploids, he can never truly rival X and Zero, as they possess the ability to hesitate and make choices, unlike Sigma, who is bound by his programming.
Unlike the original, Copy X is a Reploid without consciousness, merely following his programming. Being the copy of a legendary robot, he felt his moral code was infallible, emulating a higher good which he could not grasp, his ultimate armor being a seraph. His obsession with perfection and purity, enabling his warped sense of justice, caused his inevitable downfall. Yet, even though you don't see much of him throughout the game, you can make a lot from his views.
However, another ending called "Zero Awakened", was initially the intended canon ending of the Mega Man X series: an amnesiac X loses any memory of Zero and follows a newfound purpose that would inevitably go awry, the creation of "Neo Arcadia" would come to fruition sooner than expected, and all within his extended lifespan. This ending was intended to fork toward the Zero series, as the original X was, then, intended to be the main villain of the Zero series up until Capcom's aforementioned intervention.
You get an intro scene that sets the scene for why you've got to go fight these villains, you will fight for a good long while, then once you beat the final boss, there'll be an outro that sets the plot of its next game. Simple enough, we have a hero, a villain, and characters in a setting, much like an action figure set of the 80s such as "He-Man and the Master of the Universe", the Mega Man characters are above all else action heroes with their own action figure lines, the rest.. is ultimately up for you to decide.
As a result, the player theorized many plot holes, such that a lot of the game's flawed story-telling makes clearer sense once you make light of them using your own's imagination.
