Upon destruction of the Multipurpose Weapon in Panic Puppet Zone and complete freedom of the Flickies, Dr. Robotnik manages to catch Sonic the Hedgehog and transport him into a factory room (which appears like one in the Sega Saturn version, while the Sega Mega Drive version is a pitch-black void), which contains a series of five different machines, which must all be fought twice with only 6 rings.
- Laser Machine: A machine that fires lasers from its fingers.
- Lava Machine: A machine that uses more aggressive fire than uses in the previous incarnations.
- Spike Hands Machine: A machine with detaching spike hands that attempt to crush Sonic.
- Missile Launcher Machine: A machine that uses the same laser fingers to fire six homing missiles.
- Bouncing Projectiles Machine: Finally, a machine that fires bouncing projectiles similar to previous incarnations.
In all of these phases, Robotnik will eventually decide to lower his machine into the grid, allowing a chance to attack once. In total, the multipurpose hovercraft requires ten hits until defeat.
Upon defeat of all weapons, players are treated to the good ending, where Sonic has freed all of the flickies from Flickies' Island.