If we want to do the whole Shadow/Adventure 2 story with the next movie, just have Robotnik obsessed with cloning Sonic, using the quill he should still have from the end of the first movie. Shadow could be deemed a failure and abandoned as he continued his quest for the Ultimate Lifeform. You'd have to fudge the whole Gerald and Maria thing, maybe have them be the scientists in charge of looking after Shadow in a similar way to Donut Lord and the other human characters are treated for Sonic. Then when GUN gets involved and shoots her Shadow can show his potential and either be a rogue entity, or be tricked by Eggman again. Either way I want some sort of space located death object with his face. Be it the Ark or the Death Egg, I don't care. Though I would rather prefer a Sonic CD adaptation, where instead of Little Planet being harmed it's Mobius or whatever it is called where Tail's came from when he crossed portals. We can be introduced to other Sonic characters as background citizens. The main plot would be Eggman harnessing the energy from their world by building eggmanland or whatever mechanical district to harness the energy while Sonic and Tails go stop him. Knuckles can be involved, but I would prefer he stay with the master emerald or whatever. Eggman makes Metal Sonic who then kidnaps citizens, one being Amy who we have learned to know over the plot of the movie. The two humans can be brought over and left with a B plot where they get involved with helping look for something, throwing the Chaotix detectives into the mix, while Amy act as the leader of the home group until metal get involved in act 3. Either way, they have several places they can go after this movie. I can't believe we're living in a timeline where a live action Sonic movie is the best aspect of the franchise in recent memory.