This zone takes place on several G.U.N. naval aircraft carriers and battleships out on the sea. As such, various G.U.N. mechs such as the Gun Hunter appear as enemies as opposed to Egg Pawn models. Throughout the level, the player advances using pipes and mechanical cranes, as well as steam-catapults on the ship decks. It resembles Metal Harbor from Sonic Adventure 2. Another level that Huge Crisis shares some similarities with is Metropolis Zone from Sonic 2, with hazards like crushing pistons and jets of steam. Similarly to Mirage Road, as well as the usual fast-paced sections, there are rooms that trap the player inside. The player must defeat a set number of robots that appear to advance. The music for Huge Crisis is "Jeh Jeh Rocket".
When playing as Sonic, Special Generators appear throughout this Zone which can warp the player to the fifth Special Stage for a chance to collect the grey Chaos Emerald. As Blaze, the cyan Sol Emerald can be found after defeating the boss.
The boss of Huge Crisis is Egg Hammer Fortress. It is fought at sunset on the deck of a docked G.U.N. battleship. To defeat Sonic or Blaze, the boss will use its head to try and pulverize them, but because the head is also the cockpit, this move leaves Eggman or Eggman Nega vulnerable to an attack. It will also occasionally drop its head and use the ship's cannons to fire missiles, either aiming at Sonic or Blaze or in a completely random pattern across the stage.