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1. If tails/knuckles are in this (Which I'm pretty sure they will be), they should be held captive by Robotnik in a somewhat Sonic advance 2 approach.
Like, Robotnik is holding tails/knuckles captive in his machine, except for to save tails/knuckles AND defeat Robotnik, you have to defeat his machine a different way than normal (Somewhat like the last chaos emerald in Sonic Pocket Adventure)
2. Episode 2 should literally take RIGHT OFF where episode 1 ended.
Like you start off with the cutscene of Splash hill, like the ending of episode 1. Except maybe robotnik comes and attacks you (in a new machine, not a rehashed one), and you get into a sudden Super sonic vs robotnik boss fight.
It'd be easy of course, since it's the first battle, but this is more of like an interactive cutscene. Because after you defeat robotnik, Metal sonic comes and steals all the chaos emeralds, leaving Sonic to fall into an unknown place. Thus starting the first act of the first zone.