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Sonic the Hedgehog is an ongoing comic book series published by Archie Comics, based on the Sega video game franchise and featuring the character of the same name, since May of 1993. The series has had many spinoffs, including the still ongoing Sonic Universe which began in February of 2009.
Whereas Worlds Collide has had no lasting impact for the Mega Man comic, the issues of Sonic the Hedgehog, following the crossover are dealing with the repercussions (due to Dr. Eggman interfering with Sonic's attempt to restore their world), as well as Sonic Universe containing a follow up.
As of May 2015, the series along with Sonic Universe and Sonic Boom will be crossing over with Mega Man in the 12 part storyline Worlds Unite.
Sonic the Hedgehog #226-229 made up the storyline Sonic: Genesis, with #230 serving as an epilogue to the story. A portion of #229 was reprinted in the second half of Sonic the Hedgehog #250. The storyline itself, was referenced several times throughout Worlds Collide, as well as introducing the Genesis Wave.
The later half of the story was reprinted along with the later half Mega Man #23 in the 2013 FCBD flipbook. Dr. Wily is mentioned by Dr. Eggman as Albert, in the same way that Wily referred to Dr. Eggman as Ivo. As with the end of the Mega Man issue, the story ends with the Genesis Wave taking effect.
As with Mega Man #28, this issue serves as a Worlds Collide aftermath. As with the beginning of Mega Man #28, the issue starts of with Sonic recalling past events as his world is restored. The remains of the Egg-Wily Machine X is shown. Dr. Wily is referenced as Eggman blames "Al" for everything that happened. Mega Man is vaguely alluded to in the issue several times:
Upon returning home, Sonic hopes "that the kid got back to his home okay".
After regaining memories of the event, Tails recalls that he and Sonic "met those robots from that other universe".
The Off Panel strip (See Off Panel section below) has Sonic eager to return home after Worlds Collide, only to remember the problems befalling his friends (Sally Acorn being roboticizied, Bunnie Rabbot-D'Coolette being deroboticized & missing and Antoine D'Coolette being injured). This prompts Sonic to crash at Mega Man's place (referring to him as Rock).
These 4 issues made up a storyline titled "Countdown to Chaos". Sonic's world is slowly suffering from the usage of The Genesis Wave, while Sonic explores more of the altered history caused by Dr. Eggman. The Egg-Wily Machine X is shown in a flashback during #253, #255 and again in #256.
Dr. Eggman is revealed to no longer have the Cacophonic Conch (an instrument which controls the Deadly Six) due to the time reset and tries to recall the actions leading up to it (prompting a flashback with Wily and Xander Payne shown from behind).