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Using Chaos Control in order to enter the level from either Prison Island or The Doom, Shadow drops onto the steel-plate floors to find himself faced with... himself. The Ultimate Lifeform has popped up right in the middle of a squadron of Shadow Androids. While existentially hazardous, Dr. Eggman doesn't spot him while lecturing the troops on his Egg Mobile. After the Eggman Fleet has been dealt heavy damage by the Black Arms in Sky Troops, Eggman is falling back to his base to formulate a new strategy. However, the Doctor finds himself pursued by G.U.N. forces, which are not wasting an opportunity to attack the Eggman Empire while Eggman is already weakened.
The vanguard of the GUN forces is accompanied by E-123 Omega, likewise determined to kick Eggman while he's down. Omega wants Shadow's help in shooting down the Egg Balloon. Shadow can help Omega, or abet the fat man's retreat by knocking out the GUN forces. The neutral option is to ignore them both and just hasten inside Eggman's base. Regardless of the route Shadow takes, they face the Egg Breaker as the boss. Before the fight, Shadow asks Eggman if he is an android just like those from the start of the level, to which the Doctor lied in telling him "Yes."
This section requires an expansion.
The following weapons can be found in Iron Jungle:
The Secret Door is located in a room right after the second Save Point. Upon entering, there will be three robots. Turn around and the Secret Door is right there. Behind the door are three 4-Shot RPGs.
If the Secret Door has been unlocked, take the 4-Shot RPGs and shoot the Egg Balloon while descending with the parachute. Once Shadow is knocked off, out of ammo, or reaches the ground, jump off the platform and fall into the bottomless pit. Shadow will be put back to just before the door, allowing the guns to be picked up again. The Egg Balloon will also have reset, though it will still have all damage dealt prior to dying. This can be repeated as many times as the player has lives for massive amounts of easy damage.
The boss of Iron Jungle is the Egg Breaker, one of Dr. Eggman's machines. The guide for this battle is Omega.
This boss attacks the player with lasers shot from the machine's eyes, sitting in the center of the arena while doing so. Once the Egg Breaker's Health Gauge is depleted half-way, it will begin to attack with the mace attached to its right arm.
Although the player is required to defeat 28 GUN troops in the Dark mission, there are actually 29 GUN Troops in this Stage, with this including the Gold Beetle.
If Shadow is accompanied by the Egg Monitor while fighting one of the Big Foot Type A, the Doctor will remark "That's just like the Big Foot from Prison Island!" Eggman seems to be confusing this mech with the B-3x HOT SHOT, a similar robot which was faced by Shadow in Sonic Adventure 2.