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X first appeared in the story, "The X-Factor: Part 1". The story is set mere months before the original game. Having been created by Dr. Light, X was sealed in a capsule to analyze his systems and ensure that he would be stable. Unfortunately, Dr. Light's advanced age meant that he wouldn't live long enough to awaken X, nor was there anyone left to continue the project. As such, 100 years later-70 years longer than the process was intended to take-X was unearthed by Dr. Cain while the latter was doing an archaeological expedition. He later witnessed the creation and mass-production of the Reploid race, but grew worried about whether or not the Reploid development was going too fast, due to necessitating thirty years for his own development to ensure he didn't malfunction and end up a disaster for all. In Issue 35, the second part of "The X-Factor", Mega Man X received news of a Maverick attack, with a confirmed human casualty, and that the Mavericks responsible were put down with great difficulty. Mega Man X was disturbed by the news, as it meant the Maverick outbreaks result in the deaths of both humans and reploids. He eventually met with then-Maverick Hunter commander Sigma, who offered him a place amongst the Maverick Hunters, which X declined.
X later dealt with two members of the Emerald Spears, and grew disturbed after learning from Zero their past and motives, due to the implications that a similar event happened in the distant past to the recent events of Reploids going Maverick. He also appeared in the end of the comic, where he and Cain, unearthing the mesa laboratory that Mega Man, Bright Man, and Pharaoh Man entered a century earlier, found the Wily Walker. He later attempts to hold off the Wily Walker long enough for the Maverick Hunters (composed of Zero, Vile, and three unnamed Reploids) to arrive and engage it. Afterwards, upon their arrival, he then is instructed to regroup with Dr. Cain to see if he had found anything relating to the Wily Walker. Upon arriving, Dr. Cain informs X that he found a capsule containing information about the Wily Walker, and also reveals that the Wily Walker weapon contained chemical weapons. X then rushed back to the Maverick Hunters and helped participate in the battle, warning them of the discovery.
X as well as Zero reacted with horror when Vile, in a desperate attempt to prevent the Wily Walker from escaping, ended up endangering innocents by blowing up a bridge. X then went to tend to the wounded, and discovered a man who apparently died in it. He was then confronted by Xander Payne, who mistook him for Mega Man and accused him of leading the robot revolt. X then recognized him as being an Emerald Spears, shocking him for it existing into the century. He then left to battle the Wily Weapon, mostly to keep an eye on Vile thanks to his erratic behavior. He later was tasked, alongside Zero, Vile, and the other Maverick Hunters, to distract the Wily Weapon while Sigma personally confronts the weapon to disarm its chemical weapons. Unfortunately, the Wily Weapon began arming just that kind of weapon upon witnessing Sigma's presence. X then aided in distracting the Wily Walker with Zero and Vile while Sigma confronted it, eventually damaging it enough to take it down before it could release its chemical weapons. He also witnessed Sigma and Vile's conversation where Sigma implied agreement with Vile's assessment of humanity being inferior to Reploids with some concern, before Sigma states that their being inferior is the reason why they must protect humanity.
Eventually, as Sigma and Vile's conversation ominously implied, Sigma eventually turned Maverick, resulting in X having to fight multiple times to stop him. X arrived at the Maverick HQ as the room was in a commotion and was confused about the orders Zero was giving and proceeded to ask Zero what was going on after confirming that Dr. Cain was all right as far as he knew. X upon learning this was in denial, and believed they should contact Sigma to see what's really going on. However, after Zero, in a fit of irritation of the events going on, went into a tirade and bluntly told X that Sigma's forces are bombing Arcadia, leaving the city in flames, causing several of their forces to defect to his side and fighting the remaining Maverick Hunters, and threatening to launch nuclear missiles, X decided that he might as well aid the Hunters in stopping Sigma as an ally. He also ended up encountering the X-Hunters, which had been difficult enough to leave a bad impression on him, with Zero apparently saving him during their prior encounter. Under "complicated circumstances", X eventually ended up fighting Zero as well.
X, leading a group of Maverick Hunters to Sigma's main base, was prepared to take down Sigma once and for all. He initially was going to directly lead Zero and Axl to Sigma, although because of an ambush set up by the now-Maverick (and repeatedly-revived) Vile, only X ended up going to Sigma alone (as Zero and Axl elected to stay behind to hold Vile off). X then burst in and declared that Sigma's reign of terror was at an end. However, Sigma then proceeded to escape through a portal, although not before Sigma revealed that, in point of fact, his rule of worlds was just beginning, leaving X confused. After securing the base, X, Zero, and Axl met Silver the Hedgehog, a resident of a different dimension, who was trying to close the Genesis Portals. After Silver subdued Vile, he then gave them the coordinates of where Sigma might have gone after analyzing the computer, opening a portal for them.
However, the portal instead took them to an alternate reality to that dimension. As the portal closed off behind them, X elected to try and find locals to inquire where to find another portal-creating device. However, one of the locals, Sticks the Badger, witnessing them and believing them to be invaders, proceeded to attack them, although X managed to explain to her that they were actually cops trying to capture a criminal who escaped to a different dimension. Sticks then, after learning their true reason for coming, decided to aid them and took them over to Dr. Eggman's lair to use dimension-transport technology there (also strongarming Comedy Chimp and Fastidious Beaver to help, to X's bemusement). X expressed some concern about Zero threatening two robot locals into opening the portal, although they nonetheless managed to get to the portal.
The six returned to X's homeworld, albeit 100 years earlier than when they had left, just in time to assist the Robot Masters and Freedom Fighters with protecting civilians from the destruction of their worlds fusing. The three groups joined forces and boarded the Sky Patrol to take the fight to Sigma. Along the way, X engaged in some training with the brother he never knew he had, Mega Man, and the two discussed the never-ending battle and X's brief temptation to change history. During the trip, X helped bring the others up to speed on Sigma and his nature before Xander, Wily and Eggman crashed the meeting. He and Sonic then convinced Mega Man to let them help. The Sky Patrol then reached the Lost Hex and X helped to let the group into battle. When the Deadly Six were defeated in battle, X offered them a chance to surrender, only to be controlled by their enhanced powers until Eggman and Wily were able to neutralize them using the Egg-Wily Uppity Robot Scrambler Cannon. They were then forced to deal with a new threat: a giant Sigma and his army of Maverick clones.
Axl panicked at the sight of so many fallen foes and friends, and X had to calm him down before checking on Zero. Assured that his red-armored ally was okay, X joined in battling the Mavericks, but like the others found himself too drained to defeat them. As the majority of them began to scatter through Genesis Portals to invade other worlds, X tried to stop them only to be knocked down by Vanishing Gungaroo. The kangaroo-Maverick and a handful of others remained behind to finish off X and his teammates, only to be attacked by a group of heroic Street Fighters recruited by Sticks. Inspired by the idea, Sally Acorn directed the heroes to split into teams in order to recruit more allies and stop the Mavericks. X himself teamed up with Sticks and went over to the Ancient Steppe in the world of Monster Hunter, also being shocked that Sigma ended up resurrecting the X-Hunters before attempting to warn Felyne and Palico to flee. Eventually, a Gore Magala arrived and X nearly fought with it, although Sticks averted the conflict by convincing it to join up and fight Sigma. At the same time, Metal Sonic was summoned to bring Dr. Eggman's only Chaos Emerald to unite with those of the Freedom Fighters, so that Super Sonic could be called upon as a last resort.
Dr. Light would later see X in action due to a time travel experiment gone wrong.
In Issue 34's segment, X and Zero are excited about finally appearing in the comic, although they are escorted off by Mega Man and Roll, who informs them that they should get their own comic series as they haven't even gotten to Mega Man 3 yet. He also appeared in Issue 35's segment, where he offered to trade Sigma for Dr. Wily after Mega Man complained that the latter villain was the worst. In Issue 37, as a prank, Dr. Cain (roleplaying as a pirate) had him mark an "X" on a treasure chest, to X's embarassment. In Issue 38, Mega Man X proceeded to go on an adventure with his predecessor. In Issue 39, Mega Man X, at Mega Man's request, reluctantly explains what will happen to him in the future (as he didn't want to risk messing up the timeline), although Sigma and Wily destroy his explanation by popping out of the panel.
- Although he doesn't actually appear in Issue 41 itself, he is present in the ComicCon cover variant, manning a meet-and-greet table at a convention, with Roll approaching his table.
- X's appearances in the Archie Comics have involved two crossovers: the first with the Archie Mega Man storyline, albeit without any direct interaction with classic Mega Man characters, and the second in Worlds Unite. The latter crossover is the first crossover between the X series and the Sonic the Hedgehog franchises, as well as a number of other SEGA properties. However, X has previously encountered characters from other Capcom franchises.
- Archie Comics writer Ian Flynn admits that he did want to have X go Super while in his Fourth Armor in Worlds Unite, but Sega wouldn't let him do it.