The Doomsday Zone Sub-boss is Dr. Eggman's escape spacecraft, which he uses to flee the Death Egg at the end of Sonic & Knuckles. If Sonic has all the Chaos Emeralds or all the Super Emeralds, he enters The Doomsday Zone and undergoes a super transformation before pursuing the escaping fat man through an asteroid field.
Before catching up to the ship, Sonic has to contend with a barrage of torpedos being fired his way at the same time as dodging the space rocks. The rocket is fought in a meteor-free (and Ring-free) patch; the hedgehog has enough to contend with as three point-defence cannons spit out energy bolts and triplets of homing warheads continue to spew out of the spacecraft's launch tube. Although these munitions can't damage Super or Hyper Sonic, they can knock him backwards, costing valuable time and depleted Rings.
In order to beat this boss, Sonic has to exploit the homing torpedo's tracking mechanisms to get them to hit the boss' face. Enough damage and the ship goes down in flames... but the Doctor still isn't finished, with his escape or the Master Emerald. There is one final trick up his sleeve; the very final boss.