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This content section may contain spoilers about the plot of the comic.
Prologue: Doomsday is the first chapter of Mega Man X: Unit 49.
The story starts with X recapitulating the events since the crash of the space colony Eurasia in 2178 up to the Jakob's Incident, stating that despite Sigma being finally dead, the job of the Maverick Hunters is not over yet. X and Zero are hunting three identical Reploids with cloaks in a city nearby the 17th Unit Base with their Ride Chasers. After being hit, one of the Mavericks throw his burning cape at Zero, making him unable to evade the abandoned Ride Chaser that crashed with his. An extremely strong jamming coming from near the headquarters cuts the connection between the Navigators and the Hunters and seemed to be strong enough to prevent safe teleportations, forcing X and Zero to go back with a single Ride Chaser.
During that, two mysterious Mavericks are on top a huge Reploid sealed inside a hangar in an unknown place, and their leader waits the midnight to begin the Operation Doomsday, activating the huge Reploid and warping the three to the Maverick Hunters' headquarters.
The huge Reploid goes berserk and starts destroying the headquarters, and one of the recruits discover a way to damage him, but dies right after along with his colleagues. Meanwhile, the Vampire-like Maverick kills the personnel of the R&D Lab and kidnaps Axl, who is still in comatose and having nightmares with Lumine's speeches.Somewhere in the base, the Maverick Leader invades the room where Commander Signas resided. Their conversation reveals the original name of the leader: RD217900-6. Signas had designed a squad to hunt down him, but most of them were killed. After that, the Maverick Leader takes "something that delighted him" from Signas.
X and Zero finally arrive at the headquarters, but it is already too late and the base is in ruins. The Maverick Leader appear with his minion and a Hangerter. In an act of "kindness", he says that he prefers to retreat and talk with them later instead of fighting and spending the energy he would need to take the huge Reploid away from the headquarters. Angered, X shoots the Maverick Leader, who warps himself away telling X to remember he was taking two important things from them aside from the headquarters.