This fleeing spacecraft is the very last opponent of The Doomsday Zone, Sonic's story in Sonic 3 & Knuckles, and the Death Egg Saga as a whole (at least, before Sonic 4). After being defeated on the Angel Island and on his orbital battlestation, Dr. Eggman flees the exploding Death Egg still in possession of the Master Emerald. Transforming into either Super or Hyper Sonic, the hedgehog tears off through asteroid-choked space for one final chase.
Once the blue sub-boss has torpedoed itself into oblivion, the Egg Bomber rises up from the flaming wreckage, continuing to clutch Knuckles' Master Emerald. An Eggman ego-trip robot almost exactly like Giant Mech, this final escape vehicle speeds through the meteor field, hurling precisely the same Eggman-shaped bombs as the Giant Mech did in Sonic 2 (as well as little blue mines from its underbelly). The final robot can be defeated by just ramming it. Success with Hyper Sonic brings about the game's Best Ending, while beating it with Super brings the Good Ending.
During the final section, the level layout loops every 20 seconds or so. At the start of this loop, there is a group of six rings (3 long x 2 high oblong) in the middle of the screen (vertically). There is another group (same configuration) about 4 seconds after this a bit higher. If the player goes below the mid-line after these and grabs the groups of 3 rings, where there is a gap of no rings for a few seconds, they should head up to the mid-line again for the 6 rings at the beginning of the layout loop. The loop and 6-ring captures will vary in duration/intervals due to the scroll slowing every time Sonic hits a meteoroid plus his horizontal co-ords on-screen is defined partly by use of buttons A-C and joy left/right.