As for the story, while it's all set up in flashback, that's a necessary evil. People who don't read Sonic the Hedgehog need to be caught up to speed and people who don't read Mega Man need to be caught up to speed. Essentially, the two Doctors meet, form a new Zone called the Skull Egg Zone to build the Death Egg III and roboticize Sonic's various friends with Wily's Robot Master tech to turn them into the Roboticized Masters. It's all a lot of “getting there, getting there…” but, again, Flynn does his level best to jazz up this unfortunate necessity with some fun interactions between the two villains.