The Doomsday Zone
From Sonic Retro
The Doomsday Zone is the eighth zone in Sonic & Knuckles (the 14th zone in Sonic 3 & Knuckles). Only Sonic may play the level normally, and only after collecting at least 7 emeralds (i.e. only in Super or Hyper form). He transforms into his Super form (Hyper if you have collected all of the Super Emeralds) as the Death Egg is falling apart to catch Robotnik as he tries to escape with the Master Emerald.
Because Super Sonic must play this stage, you start out with 50 rings instead of 0, and you lose rings at the traditional Super rate of one per second. There are extra rings along the course of the level, but if your ring total drops to 0, you fall out of super form and lose a life.
To defeat the first form, drive the missiles it fires into the cockpit of the ship. After 8 hits, Eggman returns in a flying mecha, resembling the Giant Robotnik boss from Sonic 2. Keep your ring supply up by hanging back when needed, but when you feel comfortable with your ring total, hold right and hit any of the face buttons to begin ramming into him. Hitting his bombs and the asteroids slows you down. After 8 hits, the Master Emerald is freed and Eggman is beaten again. Congrats!
Also, if you look back at the fight Knuckles and Sonic had at the Hidden Palace Zone, you will see a mural hanging on the wall. It displays Super Sonic and one of Robotnik's spaceships in outer space. This method of foreshadowing is also used in Sonic Adventure, where Sonic reaches the depths of the Lost World and finds a mural displaying Perfect Chaos.
The Doomsday Zone set a precedent that would become the template for most final boss battles in future games. Among them:
Instruction Manual Description