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Base is a level when you are eggman you use the jet pack to go fast and to get to higher places to try and outspeed Sonic.exe. You have a timer of 60 seconds (which is surprisingly generous even for Sonic.exe), and if the timer reaches 0 by the time you reach the end, you are greeted with Sonic.exe before being killed. If you reach the end, you will fall in front of your 2 loyal baddies, as Eggman orders them to go after Sonic before reconsidering the fact that Sonic might destroy them both easily. Then you're given a choice:

Scratch & Grounder or Metal Sonic. Picking either one will make them go after Sonic as the unselected one follows you. Your fate depends on the choice. If you pick Metal Sonic to go after the demon, Sonic.exe emerges with it's head, before killing Eggman, as Scratch and Grounder can't mount a proper defense to protect their leader. If you let Metal Sonic follow you, naturally Sonic.exe destroys the robot duo, but since Metal Sonic is stronger than them, he is capable of protecting Eggman for just long enough for him to get into the elevator.

Of course, if you have a green ring, it won't matter, as you will be able to make it to the elevator regardless...