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The Egg-Wily Machine X was first conceived of by Dr. Eggman and Dr. Wily after they lost the Chaotix members of the Roboticized Masters. A giant battle robot that combined the genius of both doctors, it was their ultimate trump card in the battle against Sonic the Hedgehog and Mega Man. It was in development over much of the final stages of their efforts to defeat the heroes, including the final battles of the Roboticized Masters. Despite increased tension between the two, the project continued even as the heroes made their way past an army of Robot Masters, the Mega Man Killers, the Chaos Devil, and the team of Metal Sonic v3.0, Bass, and Treble. Despite the heroes' victories, the Egg-Wily Machine X quickly overpowered them in the initial encounter, and they were captured. (StH: #249, #250, SU: #53, #54, MM: #27)
The machine was subsequently forced to engage Knuckles the Echidna and Proto Man, during which the doctors were nearly defeated due to their own sabotage of each other. Unfortunately, they managed to restore and supercharge their vehicle using the power of the Chaos Emeralds, and overpowered the red heroes only to be engaged by a similarly powered up Super Sonic and Super Mega Man. After an intense battle, the Egg-Wily Machine X was reduced to wreckage. Eggman, however, managed to get his cockpit functioning well enough to allow him to attack Super Sonic during the Hedgehog's efforts to restore Mobius to its previous condition.
Eggman ultimately failed to stop Sonic from reversing the effects of the second Genesis Wave, though he did cause tremendous damage to the fabric of reality. What remained of the Egg-Wily Machine X subsequently crashed somewhere in Efrika, leaving Eggman, along with his lackeys, Orbot and Cubot, to wander back to the Death Egg Mark 2, disgraced yet again. (StH: #251, #252)
The Egg-Wily Machine X combined the best of Eggman and Wily's technology, incorporating a number of different weapons and features. These included immense strength and flight capability, as well as the ability to draw power from the Chaos Emeralds. Through this ability, it could also regenerate damage and become a super-charged battle machine. Each doctor equipped his cockpit with defenses of his own design-Wily employing "fifty thousand volts of protective shielding" while Eggman favored "death lasers"-but none of these were seen in action due to the doctors' mutual sabotage. The machine did employ a number of laser weapons and egg-shaped bombs-designed to resemble Easter eggs or Eggman himself. Despite this formidable arsenal, it was not as powerful as two beings who had undergone Super transformations. The Egg-Wily Machine X was also designed to incorporate both doctors' flying vehicles.
- As noted by Dr. Eggman, the Egg-Wily Machine X is a combination of concepts from both Eggman and Wily's combat vehicles. Eggman's vehicles tend to have the prefix "Egg" in their name-such as the Egg Hawk-while Wily's vehicles are typically known simply as "Wily Machines."
- When working to fix the Egg-Wily-Machine-X, Eggman mention's "battle" and "chase" programs, a reference to the raceing game "MegaMan Battle & Chase". Wily then mentions a "M.B.M." circuit board, which is a reference to "Robotnik's Mean Bean Machine".