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The original Death Egg was launched from Westside Island, but due to Sonic's efforts where he defeated Silver Sonic and Dr. Eggman, ended up crash-landing on Angel Island. Dr. Eggman enacted repairs and managed to launch the craft yet again, only for Sonic and Tails to bring it down. A second launch from Angel Island was accomplished using the Master Emerald as a power source, but Sonic once again brought the flying fortress down, this time for good. Some time later, Eggman constructed a second version, this time building it around the Little Planet, but his plans were thwarted yet again by Sonic and Tails. (StH2, StH3, S&K, StH4)
- From a reader's perspective, this picks up from where the original Pre-Super Genesis Wave continuity left off.
After the events of Worlds Collide, Eggman and his lackeys returned to a completely new (to them) timeline, in what was left of the Egg-Wily Machine X, which crash landed in the middle of the Efrikan plains. As a result, the doctor's most recent Death Egg had been left unmanned in Artika, while a Shield Generator was being designed for the vessel in the Metropolis Zone. However, Bunnie Rabbot-D'Coolette and two of her fellow Knothole Freedom Fighters stole the shield generator for their Sky Patrol base. During the doctor's absence, his forces had to deal with Sally Acorn, who had penetrated the ship as part of a mission to steal Egg Network access codes. By the time Eggman and his lackeys returned after a lengthy misadventure, Sally had already escaped, but not before being caught on the security tapes. Enraged over how he'd lost his Roboticized weapon (having just come from an alternate timeline where Sally had become his robotic slave), he launched Metal Sonic to hunt her down, determined that Sonic would not see her again alive. This assassination attempt was thwarted thanks to Sonic's efforts, but upon accessing his vessels' scanners Eggman soon realized that larger problems loomed: the entire planet broke apart as a result of the improperly reversed Super Genesis Wave. After launching the craft to escape the cataclysm, Eggman determined that no means existed of reversing the changes to reality, leaving him apparently stuck with a broken world. However, he soon discovered information about Professor Pickle's research on the Gaia Manuscripts, and dispatched E-106 Eta and its Badnik Horde to capture both the professor and his research. (StH: #252, #253, #254, #255, #256, #257)
Later, Eggman was contacted aboard the Death Egg by Cassia and Clove, Egg-Boss sisters who reported the loss of a Chaos Emerald previously held in Crystal Cave. Realizing that Sally must have learned of the Emerald from his stolen files, Eggman contacted Egg Boss Thunderbolt with orders to retain a Chaos Emerald she had come into possession of in order to lure the Freedom Fighters into a trap. While the Freedom Fighters were en route, Eggman launched an attack against the Sky Patrol using his War Walrus, but was defeated by the superior arsenal of the Freedom Fighter craft. Thunderbolt subsequently reported the failure of her attempt due to Sonic's unexpected transformation into the Werehog, infuriating Eggman. However, he subsequently learned that the planet's shattered condition had strained the resources of his enemies and allowed his forces to seize more territory, and that the energies of Dark Gaia released by the cataclysm were greater than any other measurable energy source on the planet. He thus determined to gather the Chaos Emeralds and secure the Gaia Temples in order to prevent anyone else from restoring the planet, allowing him to process the Dark Gaia power. Another Chaos Emerald located by his forces in Soumerca was secured despite the Freedom Fighters' efforts to seize it, and Eggman managed to get a Tails Doll aboard the Sky Patrol despite their escape. His success was brief, however, as the Hooligans boarded the Death Egg with news that they had lost a Chaos Emerald to Knuckles the Echidna and the Chaotix. As such, Eggman ordered them to enter the Chaos Emerald Championship to make it up to him, and added a directive of sabotage after failing to convince Breezie the Hedgehog to turn her Emerald over to him. (StH: #263, #265, #266, #267, #268, SU: #66)
The current Death Egg is equipped with advanced scanners and powerful communications equipment. It also has a protective force-field that surrounds the ship's hull and can produce powerful waves of energy that can bring down enemy aircrafts.
- The Death Egg is a blatant parody of the Death Star from Star Wars.
- The Death Egg was first featured in the video game Sonic 2 and later reappeared Sonic 3 and again in Sonic & Knuckles, with a second version appearing in Sonic the Hedgehog 4, and the same craft or new ones appearing in subsequent games. Due to the effects of the Super Genesis Wave, the history of the various Death Eggs more closely matches those of their game counterparts, though with various exceptions. Head writer Ian Flynn, in response to a fan query, noted that at least two or three Death Eggs have existed in the reboot reality, possibly more. ()
- The current Death Egg has a striking resemblance with the Death Egg from Fleetway's Sonic the Comic.