The Operation Doomsday is the Maverick attack lead by Saturn, who activated and put in berserk a huge Reploid, then teleported him with a vortex to the 17th Elite Unit's Base, shown in Prologue: Doomsday.

The Maverick Hunters were apparently baited by a trio of Mavericks so they would be far enough of the base, and then jamming devices were activated near the headquarters so the Operators couldn't communicate with Mega Man X (character) and Zero, also preventing any teleport by the common method.

The Operation resulted in the destruction of most part of the Maverick Hunters' main headquarters, the death of several low-Class Hunters, the disappearance of the Maverick Hunters' leader Signas, the kidnapping of Axl, beyond-repairs damage to the Operators Layer and Pallette, and the beginning of the Great Neo Maverick War.