Robotnik pilots a small rocket with spikes on the top. Once Sonic finds him, the only option is to attack by hitting his rocket. The doctor will become angry and will fly into the ceiling, causing blocks to fall onto the floor. The player must jump on top of one while Robotnik electrocutes the floor, without harming the pieces of the ceiling. The blocks fly into the air, and the player must reach the next floor level. This process repeats a few times, as the amount of floor decreases and eventually spikes fall, until he/she reaches the final roof and can defeat the scientist. Robotnik will not escape on his Egg Mobile this time, but will instead run away from the scene while the rocket finished exploding. In the bad future, the Wacky Workbench boss is gray and in the good future, it is purple.
When facing this boss as Tails in the 2011 remake, Tails' maximum flight time is severely reduced for the duration of the fight, to prevent the player from simply flying up and hitting the boss immediately without using the blocks.