The level would not be a part of the regular level progression, but instead would be reached by taking a secret exit in Tidal Tubes Act 2 (maybe only Tidal Tubes Act 2 Past?). The boss could remain the same (with a background looking like an underwater cavern instead?). Upon completing the boss battle, Sonic (or Tails, or Knuckles) moves to the new zone.
Upon completing the new zone, Sonic is dropped in front of the Sunken Saucer and enters it. At this point, one of two things can happen:
If the zone is finished in the future, upon entering the Sunken Saucer the regular level progression resumes.
If the zone is finished in the past, Sonic enters an otherwise unreachable past version of the Sunken Saucer. The zone itself is slightly darker or tinted differently using a shader, but is otherwise completely unchanged (I can even imagine reusing the music). When Sonic reaches the altar where Metal Sonic revives Eggman during normal gameplay, Metal Sonic arrives and a completely new final battle starts.
During the battle either Metal Sonic triggers back and forth time travels (it could be interesting to design a phase around this concept?), or both Sonic and Metal Sonic are sent back to the future between two phases for any given reason. Either way, by the end of the battle, both should be in the future. For the ending to make more sense (see below), if Sonic has all Emeralds and all Time Stones, the battle has an additional phase.
The battle ends with Metal Sonic being destroyed for good before even getting a chance to resurrect Robotnik, and the Saucer short-circuiting and powering off. Sonic then runs off screen. In a bit of a playable epilogue, Sonic emerges in a map that is used for TTZ -> SSZ transition, only with added platforms to allow Sonic to go up, and with a bright sky to represent the dawn of a new day :D . Once Sonic reaches the top and goes slightly to the left (aka as soon as the wall on the right is no longer visible :) ) a cutscene triggers in which, just like they dropped him off in AAZ, Tails and Knuckles fly in to pick him up.
The credits screen appears in reverse: it starts with the camera showing the Little Planet, intact, then pans down to Never Lake, and then follows Sonic, Tails, and Knuckles as they fly from left to right. After the credits roll, the camera pans down and goes underwater, with the screen quickly going from displaying a bitmap image to a solid blue, to a solid black. That's when the message "Sonic, Tails, and Knuckles continued the fight..." is shown if it applies. The camera pans down to a broken Metal Sonic in a poorly lit room (floor of the Sunken Saucer) short-circuiting, just like in the regular best ending.
If all Chaos Emeralds and Time Stones are collected, Metal Sonic turns off just like in the original ending.
Otherwise, after a second or two Metal Sonic stops short-circuiting, "Try again" appears on screen, a sound similar to the one at 1:28 in this cutscene https://youtu.be/-DynbmAehL8?feature=shared&t=88 starts droning and gets louder and louder, Metal Sonic's eyes light up and the screen turns red.
An idea for reusing the lost Time Twisted zone presented in Overbound's livestream from December 10, 2023 ( https://www.youtube.com/live/jm3wC2C9VPY?feature=shared&t=1219 ):
The level would not be a part of the regular level progression, but instead would be reached by taking a secret exit in Tidal Tubes Act 2 (maybe only Tidal Tubes Act 2 Past?). The boss could remain the same (with a background looking like an underwater cavern instead?). Upon completing the boss battle, Sonic (or Tails, or Knuckles) moves to the new zone.
Upon completing the new zone, Sonic is dropped in front of the Sunken Saucer and enters it. At this point, one of two things can happen:
If the zone is finished in the future, upon entering the Sunken Saucer the regular level progression resumes.
If the zone is finished in the past, Sonic enters an otherwise unreachable past version of the Sunken Saucer. The zone itself is slightly darker or tinted differently using a shader, but is otherwise completely unchanged (I can even imagine reusing the music). When Sonic reaches the altar where Metal Sonic revives Eggman during normal gameplay, Metal Sonic arrives and a completely new final battle starts.
During the battle either Metal Sonic triggers back and forth time travels (it could be interesting to design a phase around this concept?), or both Sonic and Metal Sonic are sent back to the future between two phases for any given reason. Either way, by the end of the battle, both should be in the future. For the ending to make more sense (see below), if Sonic has all Emeralds and all Time Stones, the battle has an additional phase.
The battle ends with Metal Sonic being destroyed for good before even getting a chance to resurrect Robotnik, and the Saucer short-circuiting and powering off. Sonic then runs off screen. In a bit of a playable epilogue, Sonic emerges in a map that is used for TTZ -> SSZ transition, only with added platforms to allow Sonic to go up, and with a bright sky to represent the dawn of a new day :D . Once Sonic reaches the top and goes slightly to the left (aka as soon as the wall on the right is no longer visible :) ) a cutscene triggers in which, just like they dropped him off in AAZ, Tails and Knuckles fly in to pick him up.
The credits screen appears in reverse: it starts with the camera showing the Little Planet, intact, then pans down to Never Lake, and then follows Sonic, Tails, and Knuckles as they fly from left to right. After the credits roll, the camera pans down and goes underwater, with the screen quickly going from displaying a bitmap image to a solid blue, to a solid black. That's when the message "Sonic, Tails, and Knuckles continued the fight..." is shown if it applies. The camera pans down to a broken Metal Sonic in a poorly lit room (floor of the Sunken Saucer) short-circuiting, just like in the regular best ending.
If all Chaos Emeralds and Time Stones are collected, Metal Sonic turns off just like in the original ending.
Otherwise, after a second or two Metal Sonic stops short-circuiting, "Try again" appears on screen, a sound similar to the one at 1:28 in this cutscene https://youtu.be/-DynbmAehL8?feature=shared&t=88 starts droning and gets louder and louder, Metal Sonic's eyes light up and the screen turns red.