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?
None of my doubts over the initial sealing lasting a full 100 years in the final scheme of things have abated, where RZOCW mentioned only half a century of study, and X's hardened sadness portrayed as relating directly to his concurrent removed state. I don't intend to rehash since nothing really new has been learned about that since the last argument that I'm aware of, I'll just agree for now that the first sealing possibly could have lasted 100 years, and X certainly did face tough battles without Zero during this time.
As of Z1, the Irregular Wars officially closed some 100 years before the setting of the game, according to Z1's Official Guide Book. However, that closing period was not the end of all incidents, fighting, and hardships, which continued seemingly throughout to the more recent time, when Neo Arcadia was finally established and became the paradise of humans at the cost of repliroid rights, and the battle focus turns to Neo Arcadia government vs Resistance political terrorists. Copy X asserts that the current state of humans in Neo Arcadia is better than anything that Original X or Zero had or could accomplish, thanks primarily to his own efforts. If we assume that Ciel creating Neo Arcadia and Copy X were true plot intentions, Neo Arcadia arose within the last decade before the game began, and the Original X had little to do with its foundation but laying the groundwork of battling to ensure the survival of man and repliroid in the meantime. Later Z2-onward revelations re-established X as the city-state's founder and Ciel's language became figurative as she herself a product of Neo Arcadia policy.
Yet before a Copy X was established, and before Ciel was the progenitor of him, a very different scene was possible, where Neo Arcadia could have been fashioned 100 years ago following the war by the one and only X, and the gradual deterioration from ideal stronghold of hope to reploid living hell would have played out over a longer, more gradual period. I think this was the intention, even after, and why it was returned to eventually, that Neo Arcadia was X's baby born of light and hope but was eventually swallowed by darkness and despair, and why they returned to it in the aftermath of the Z1 to Z2 transitions.
The occurrence of hard lonely battles taking their toll on X's purview seems the same regardless of the Copy's introduction, but the change of characters directly affects how X responds to this stimuli. Instead of choosing to rest and work on his resolve, ducking out of sight and leaving the responsibilities of the world to others for a time, it initially would have hardened him to accepting what he believes the lesser of 2 evils and foregoing reploid rights for the sake of human peace. Both decisions are contraversial, but X's choice to remove himself, though sombre, is in its own way more of an action of holding on to hope, whereas the decision to instill martial law upon reploids seems to be resigned acceptance that only through active force can "peace" be maintained, a quite fatalistic and harrowing viewpoint where the expectancy for equality and freedom has died. I'm glad this dark decision was changed, feeling that X desires better than that. Z1 left X's manner of self removal a mystery, but X's speech sounded as if he could and eventually intended to rejoin the world once his mental strength and fortitude was renewed.
Since the Dark Elf is the source of most changes to the timeline, and the Dark Elf used to be Mother Elf, the origin of Cyber Elves, I do wonder, how much of this premise existed during the creation of ZERO.
Concept art notes explained the initial concept of Cyber Elves as Replisouls. Some speculate then that early on, the Cyber Elves were all going to be repliroid ghosts, either from the Irregular Wars, or from Neo Arcadia's harsh policies. Replisouls could be linked to the very "human-like new type" repliroids who made up the Resistance. (Connecting the powers of the old generation of reploids to be used by the new, sounds a lot like X8...) Ciel, as a Soul Summoner, would have the ability to rally these souls and aid Zero through something called Soul Battle, perhaps how he himself would interface with them. She may have even been responsible for summoning Zero's soul back from the void, in the pre-X6 concept realm before Zero was already revived and sealed as a starting point.
RTRZ info mentions that Cyber Elves had some link to past incidents and their appearances aren't currently understood. This is often considered to be the first hinting of the Elf Wars as part of the lost history of Neo Arcadia. Considering that initially they did not plan to have a sequel game, the origins of Cyber Elves would likely remain simply as a miraculous new technology without further exposition. Yet within a month after game release, it would seem the rough concept around a potential Elf Wars and maybe even the Dark Elf existed as well. The known concept art for the Dark Elf is said to be from Zero 2, as opposed to the concept art of the Big 4's Armed Phenomenon forms which we're told are sketches from Zero 1 that went unused until the sequel. So, Dark Elf herself probably was not conceived or considered to be used until sometime after a sequel work was approved, shortly after Z1's release. But some believe that a benevolent Mother Elf type figure as origin of the Cyber Elves would have been used in Cyber X's stead as Zero's magical plot aid. Nothing I know of was ever shown to evidence this, it seems to be more of a fanon answer to the question "If the last boss was actually the real X, then who would the Cyber-X role have been?" But other answers exist to that, possibly Passy or Ciel would have had larger roles, or on a far darker scale, that Cyber-X would have still been the real X, using his powers to communicate. In that case, X would likely have given Zero the saber to destroy Ciel with, but he uses it to destroy the Golem instead. Then X appears again after Zero has proven himself too much of a trouble, and gives Zero the key and issues him a challenge/invitation to attempt to infiltrate Neo Arcadia's toughest security area, thinking that he'll take care of Zero personally this way.
Sometimes I think it's easier to view this list as Neo Arcadian propaganda, or as an element of the mythology surrounding the founding of the nation. Legendary weapons of power, now wielded by the stalwarts of Neo Arcadia, it's a beautiful and epic idea. The nature of mythology is always embelished, legends get confused and rewritten in the passing of time, and the idea that the generals are using holy relics as weapons gives them an even higher aura of respect and invincibility. Truth can't in this respect stand up to what captures the popular imagination or serves the public good.
On the other hand, there's the idea that they were not originally the Big 4's weapons, but were later imparted to them when battle was required. Whose weapons they were before would be a huge mystery, though perhaps the easiest explanation might be that they were all X's weapons. Almost like X6, X starts with X-Buster and Z-Saber, and then gains 8 more special weapons as per status quo, handhelds this time. It's the right number, although X is rarely portrayed as using anything but his own X-Buster.
On the other other hand, the weapons could have been made back then but never utilized until the Big 4 came along. Rather simple, but anti-climatic. Weapons of war that were made for Top Class Irregular Hunters, maybe not any one in particular but with the idea that this advanced weaponry could help end the wars. As a weird twist, Vile was the one working on weapons, it would be very ironic if not entirely unlikely if he had wound up being the one who revamped the Z-Saber and built the Big 4's weaponry... nah, he would have thrown that in their faces long ago. But it reminds me, the X-Buster was technically created long before Irregular Hunters existed, ergo the definition of who and what they were developed for seems a bit loose. It might have been improved in some way, as the Z-Saber was, to make that count.
Then there's the suggestion they were around and active in the late Irregular Wars, possible, although never mentioned as being so in any info material other than the Ten Shining Arms. I have the impression they were products of after the Elf Wars, after Neo Arcadia's official foundation, after Omega is bound and Vile is banished and Zero fast asleep.
Most of the time, the release of X6 (and subsequently X7 and beyond) is blamed for the convoluted state of the current ZERO series.
Perhaps we can say they both influenced and convoluted each other. X6 influenced the Zero series a great deal, but itself was a retcon of X5 as the series ender. What we might have received if X6 had not come about we'll never know, but the differences could well have been staggering.
Eurasia was given a lot of standing in Z1's materials, but the X series greatly pushed the time back and is even said to reclaim the area directly around the colony's impact site, so as to wonder whether Eurasia could still be a strong influence in global calamity. The Elf Wars gives the X series the freedom to rebuild more of the planet up again from the devastating impact of the Eurasia incident, since another globally destructive conflict will ensure that the post-apocalyptic state in Z1 comes to pass. Even so, Command Mission's creation pushes the Z series changeover much farther back than was seemingly ever intended. And then Z4 references Eurasia's crash as well, saying there are still remains of it intact and that the nature is a result of a Eurasia environmental device that continued to function, even after all that time. Did the cleanup miss an entire section, or perhaps the left part as a reminder, or saw the enviro. unit functioning and left it going in hope of return? Adds up a little strange. Axl remains a mystery, as does whomever X was fighting when he used the Mother Elf if Sigma was departed in X8. Mysteries are not necessarily plot holes, but the overuse of them without any resolution adds to the feeling of convolution a great deal.
Edit: Posted in the wrong thread, somehow. Fixed now.