The video game icons will join forces for a 12-part storyline spanning three titles after Sega and Capcom both agreed to lend their characters to the project.
Sonic and Mega Man scribe Ian Flynn will pen the story, which will play out across issues of Archie's Sonic the Hedgehog, Mega Man and Sonic Universe.
He told USA Today: "I'm already living the dream by writing the Sonic titles. Then I got to live the other dream of writing for Mega Man. With that many dreams being handed to me, I figured it was only a matter of time.
"They're both fun, adventurous and open to everyone. They both have heavy sci-fi themes, mainly robotics, underpinning them that give us something to build from and play off each other. That, and they both have mad-scientist nemeses with fabulous moustaches!"