Shortly after returning to his world following the Super Genesis Wave, Dr. Eggman encountered some of his forces in the Efrika Plains. He was quickly made aware that his military was now known as the Egg Army, with it's various regional leaders titled as Egg Bosses. This first of these whom he encountered was Axel the Water Buffalo of the Efrika Unit, followed shortly thereafter by Mordred Hood in Avalon. He next made contact with Tundra the Walrus in Artika, just before the beginning of the Shattered World Crisis. While attempting to find a solution to this development, Eggman attempted to contact one of his Egg Bosses near Spagonia but found that they were all busy trying to deal with the crisis themselves. After obtaining the Gaia Manuscripts, Eggman contacted Axel again with orders to increase security at his unit's base, as Eggman suspected that it could be one of the Gaia Temples. (StH: #253, #254, #255, #256, #257, #259)
Egg Boss sisters Cassia and Clove the Pronghorns were later tasked with recovering a Chaos Emerald from Crystal Cave, but it was stolen by the Freedom Fighters thanks to files stolen from Eggman by Sally Acorn. Before reassigning the pair, Eggman contacted Soumerca Egg Army Boss Thunderbolt the Chinchilla, who had also located a Chaos Emerald, and instructed her to prepare for the Freedom Fighters' arrival. Thunderbolt laid a trap for the heroes but was unprepared for Sonic the Hedgehog's Werehog transformation, which decimated her forces. An attempt to redeem herself by deploying the Flying Dynamo robot proved unsuccessful. Tundra managed to capture two of the Guardians of the Gaia Keys, only to lose them when Sonic the Hedgehog and Rotor the Walrus managed to infiltrate his base. Clove was later entrusted with the only one of the seven Chaos Emeralds that Eggman's forces had managed to retain through an engagement with the Freedom Fighters. (StH: #263, #264, #265, #266, #267, #276, #277)
Nephthys and her unit in Shamar later closed in on another set of Gaia Keys, only to run into opposition from several of the Knothole Freedom Fighters and the Shamar Freedom Fighters. All of the Egg Bosses would then be called upon to reclaim Eggmanland from Walter and Wendy Naugus and their minions. (StH: #278, #279)
Soon, all the Egg Bosses were summoned by Eggman for a new mission- retake Eggmanland from the Naugus Twins, Walter and Wendy. Eggman paired them into teams of two so they could do their missions. The Egg Bosses later confronted the Naugus Twins, and managed to defeat many of the brainwashed Badniks and the Witchcarters. After Walter is defeated by Eggman, Eggman makes Wendy an Egg Boss, due to him wanting an even number of Egg Bosses, plus not having an Egg Boss with magic. All of the Egg Bosses then return to their rrespective regions, while Wendy is assigned to obtain the Cacophonic Conch. (SU: #83, #84, #85, #86)
Axel and Conquering Storm later fought Sonic and the Freedom Fighters, in an attempt to prevent them from stealing the Gaia Keys they have in the possession. Thnderbolt also fought Knuckles the Echidna and Mighty the Armadillo for possession of two of the pieces of the Master Emerald. (StH: #280, #281, #282)
- The Egg Boss roster currently includes three characters who were previously Dark Egg Legion Sub Bosses in the Pre-Super Genesis Wave Timeline. Those being Mordred Hood, Conquering Storm, and a heavily redesigned Akhlut.
- The roster also includes a villain who appeared in the old timeline who was not previously a Sub Boss, that being Battle Kukku XV. Interestingly, the Battle Kukku was originally considered to be made a Sub Boss.