Disclaimer: really long post, please bear with me.As we all know, the writing process of the MegaMan Zero series was a process of constant alterations, through retcon or otherwise, having to deal with it's own contuinity and that of the X-series all at the same time. For some time now, I've been analyzing the first game in the ZERO series to figure out the source of the current convoluted canon and why things are as they are now. All in all, this just me trying to collect my thoughts on the progression of the plot from ZERO to ZERO2 in the hope of giving some nice insight on it.
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Three key moments in developement changed the face of the series forever.
-The release of MegaMan X6 by another team.
-The choice of Copy-X as the final boss a month before release.
-The writing of the sequel that was never intended.
Most of the time, the release of X6 (and subsequently X7 and beyond) is blamed for the convoluted state of the current ZERO series. Whilst certainly true, Zero went from dead to being sealed, I've started to see that most of the issues that exist today are caused by IntiCreates never having intended a sequel during the writing of ZERO and making a few hasty choices in regards to writing in Copy-X a month before release, instead of the release of X6. In doing so, a lot of plot elements are turned upside down and Inti had to 'make a few complicated explanations real fast.' There are quite a few elements that will later lead to contradictions.
Anyway, supposing familairity with the timeline as it is as of the release of MMZOCW, this is the timeline from a solely ZERO1/RTRZ perspective, I've bolded RTRZ's contribution (you can skip this quote if it gets too long:
ZERO1/RTRZ timeline:
-The fall of the giant colony "Eurasia" during the Maverick Wars (events of MegaManX5), this was the single disaster that caused the greatest degree of damage. A punishment that drove an ugly hole into mother earth, causing catastrophic damage to the troposphere, and people could not reap the benefits of the "blessings of the sea" for a long time.
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-X and Zero save the world together. (100 years before ZERO1, Zero's weapon is one of the legendary ten shining arms.)
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-Zero speaks with a scientist to have something removed from his systems, the scientist is unsure if it is even possible, but if all goes well, it will take 102 years. Zero goes to sleep and leaves future incidents in X's care. (100 years before ZERO1, Zero ending of RockmanX6.)
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-Andrew was a sailor and meets a beautiful young human lady and is touched by her singing.
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-Andrew spends time with her and they fall in love, eventually begin to live together.
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-The lone hero X ends the Maverick Wars after 100 years of fighting without Zero but has afterward mysteriously become a cyber elf. Ciel creates Copy-X and together they create Neo Arcadia at the center of rebirth. The long, drawn out Maverick Wars resulted in mankind's very existence being threatened, due to the immeasurably damaged state of the earth's environment, especially the damage caused by the Eurasia space colony. Aiming to rebuild the world of man, Neo Arcadia established two primary objectives. One, the eradication of the Iregulars who had been the cause of the wars; and two, to revive the earth's environment for expanding the region of human habitation. Therefore, from both the sea and the air a large-scale tropospheric control operation for the rejuvenation of the environment was conducted. The, Four Guardians, Big4 of X-Bioroid (Harpuia, Leviathan, Fafnir, Phantom), are created for this purpose. Operating a giant weather control mechaniloid, Harpuia brought about a blessing wind of hope to the people. From the main shaft of Neo Arcadia, Leviathan, who was created in order to bring back the favor of the goddess of the sea, used her abilities to do her part for the operation. Phantom and the Zan'ei unit act as "X"'s personal safeguard and defenders, Fafnir's current activities are unspecified.
-Andrew's life partner grows old and begins to resent her looks compared to Andrew. Ciel changes Andrew into and old man to make her happy. She later passes away.
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-The government starts fearing Reploids will become irregular, and for unjust reasons that became more and more commonplace, the Reploids are punished by disposal one after another. Ciel participated in the exploitation of the Reploids because of the government, but could not shoot those to be punished and tried to cover the stigma of Irregularity.
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-Ciel begins to live with the Reploids who have been targeted for destruction (the Resistance) and have escaped to the half-collapsed ruins of an old city, where the small ammount of energy still remaining there has kept them alive. Because of this situation Ciel, who is now the leader of the Resistance, wants to develop a subsitute energy, and because of her superior talent as a scientist, there are no alternate ideas concerning a new energy source for everyday life. One of the Reploids with the Resistance is a girl Ciel named Alouette who never felt kindness from others when she lived Neo Arcadia. Everything changed when she met Ciel, she even began to think of the importance of their existance.
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-To use military force to combat Mavericks and Resistance members who escaped Neo Arcadia to the wastelands, Neo Arcadia developed the "Scorched Earth Operation" in which extermination attacks were performed. A roller strategy involved carpet bombing, and deployment of an enormous ground force for total supremacy. These severe tactics strike terror into all Irregulars who witness it. If the fighting ahead isn't ceased immediately, they will never know another peaceful night's sleep. At the forefront of the Scorched Earth Operations, a Fafnir's form can always be made out. Likewise, iIn Neo Arcadia, those who can escape under suspicion of Iregularity are few, and those who can survive long are even fewer, because many who try to hide are quickly discovered and dealt with by the oppressive Zan'ei unit which has become and anti-Iregular, anti-Resistance intelligence unit. The other Units and Guardians also focus their attention on Mavericks and the Resistance.
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-The demonic hand of the government finally approaches even those Resistance Reploids who have lived quiet lives. They're cornered. At this rate, they will all die. Ciel remembers the name of the Legendary Reploid "Zero", who even now sleeps in a certain place.. If the legends is true, maybe he can save them. She therefore seeks out to find Zero.
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-Harpuia battles the Resistance at the remains of the laboratory called the "historic ruins." He was "hunting" the Resistance's leader, the young human girl Ciel whose capture should have proven to end the fighting. Standing in his way, was a single red repliroid; Zero. Starting the events of MegaManZERO. (100 years after Zero and X saved the world, 100 years after Zero's seal, Andrew's life partner has long since passed away, Ciel age 14)
With the release of ZERO2 and ZERO3. A lot of the above points either become invalidated or are moved around. Most notably:
-Neo Arcadia's founding. (Current event, ZERO1 - 100 years ago, ZERO2+)
-The Big4's creation. (Current event, ZERO1 - 100 years ago, ZERO2+)
-Zero's being sealed twice. (Introduction of Elf Wars inbetween two 100 year gaps instead of a single 100 year gap from X6 to ZERO.)
The biggest reason I find for this is: Dark Elf.
When Dark Elf is introduced into the plot, IntiCreates found themselves with a small issue; the Maverick Wars ended quite recently, likewise, Neo Arcadia is made quite recently as well. But, Dark Elf is a rather mysterious force, like mythological. As such, Dark Elf is said to be 100 years old. And then, with the antagonistic forces of Omega and Weil applied, as well X's mysterious dissappearence; Neo Arcadia suddenly has a centennial history under its ruler X.
The above choice of a centennial history changes the timeline completely; Neo Arcadia and the Big4's time of creation gets increasingly confusing, Ciel gets some quick explanation on how she made Neo Arcadia whilst it already existed, X's sealing of Dark Elf is somewhere in timeline limbo and Zero suddenly has to undergo two sealings.
Going by the above premise, this is why we got two sealing events instead of one, a direct result of Inti's desire for super contuinity with X's final words during the first game:
With a founding of 100 years ago, Zero could be present to end the war. However, the story is clear; X is a lone hero that ended the war and fought for 100 years without Zero. Despite this, X and Zero saved the world together, 100 years ago? How can X fight for 100 years when there is no war after Neo Arcadia's founding? How can X be a lone hero when Zero wasn't sealed yet? How can X and Zero save the world together when X is a lone hero that ended the war, and fought a century without Zero?
This direct contradiction is the cause for nearly every change revolving around Zero and Omega's backstory. There was only one conclusion to fix the above; Elf Wars and two sealings.
From X6's ending to Elf Wars, 100 years. From Elf Wars another 100 years to ZERO, with Omega and Zero's innate relation right in the middle of all that. All of this is the strange outcome of one change having long lasting effects on everything else.
In a similar case, Mother Elf's very existance as the Sigma Antibody Program demands that Mavericks can't exist in the ZERO timeframe, yet Neo Arcadia fearfully deems all Reploids as a Maverick. In order to explain this ungrounded fear, Inti took the simple concept of the Resistance's substitute energy and turned it into the large scale energy crisis which led to the unjust retirement of Reploids under a bullshit explanation of Maverick behaviour.
I hope the above gives some nice insight in why the series turned out as it did. There's a lot more material to cover, such as how some changes affected the Big4 and other details such as the Shining Arms, but this had gotten way too long. By primary point is how X6 and the other X-games are not really to blame for the convoluted state of affairs; they do add to it, but are not the primary cause. I feel that what happened with the story was mostly unavoidable and a result of too many grandiose ideas limited by a game by game release basis.
If anybody has any alternate hypothesis, feel free to share.