Here's one minute problem with that: Sonic, not Tails, flies the Tornado and catches Knuckles. Also, I might be mistaken here, but I'm pretty sure Knuckles's Sky Sanctuary Zone comes after Doomsday Zone chronologically. As in, after Sonic gets back the Master Emerald from Eggman, it falls down to Sky Sanctuary into the hands of Metal Sonic v3 and the "Knuckles path's antagonist" Egg Robo. Then, after Knuckles defeats Super Metal Sonic, Sonic catches Knuckles, and then the Master Emerald is returned to Angel Island Zone. Plus, Tails is a mechanic prodigy; he probably figured out a way to integrate Debug Mode into the Tornado, and by using the Debug Mode he made it all the way up to Sonic in no time flat. d= (;
No seriously though, excepting that last sentence, that's the way it went down. Someone who has a much better idea of the story's structure and integrity, feel free to correct me on this.