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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.
It starts with X recapitulating the events since the crash of the space colony Eurasia in 2178, and that their job isn't over yet. X and Zero are hunting three identical reploids with cloacks in a city nearby the 17th Unit Base with their Ride Chasers. After being hit, one of the Mavericks throw his cape and bike against Zero, revealing his image and escaping. A strong jamming cuts the connection between the Operators and the Hunters.
Two mysterious Mavericks appear over a huge Reploid inside a hangar somewhere, the leader waits the midnight and starts the Operation Doomsday, activating the huge Reploid and teleporting the three to the 17th Unit Base.
The huge Reploid goes berserk and starts destroying the 17th Unit, one of the recruits discover a way to damage him, but dies right after along with his colleagues. While this, the Batman-like Maverick kidnaps Axl, who's still in comatose and having nightmares with Lumine.
Somewhere in the base, the Maverick Leader invades the Commander's room. Their conversation reveals some things about the villain: his original name - RD217900-6 -, the Maverick Hunters already had contact with him in the past, and that Signas designed a squad to hunt down him, and most of them are dead. After this, the Maverick Leader takes something from Signas. His destiny is unknown.
X and Zero finally arrive at the 17th Unit Base, but it's already too late. The Maverick Leader appear with his minion and a Hangerter . The Maverick Leader, in an act of "kindness", says that he prefers to withdraw with the huge Reploid and talk with the Hunters later instead of staying there and letting the monster destroy what remained from the 17th Unit. Angered, X shots the Maverick Leader, who withdraw saying he's taking two important things from them: Axl and something.