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."
As Shadow seizes the fifth Chaos Emerald, his fractured memory is starting to come together again. Shadow remembers the fatal fall out of orbit after killing the Finalhazard; waking up in a vat of green goo inside an Eggman base and row upon row of other Shadow Androids, stored neatly in their own capsules. Combined with Eggman's devious insinuations through the previous course of the game, Shadow comes to a final conclusion: that he is a Shadow Android, an Eggman-made copy of the deceased original Shadow. Determined to kill his creator, the hedgehog races towards the doctor's base.
Circumstances, however, do not make things easy for Shadow. In Iron Jungle, despite most of their forces fighting in their war against the Black Arms; G.U.N. has mustered the vast firepower and resources necessary to assault the Eggman Empire. Eggman retreats into a classic supervillain active volcano hideout. Indeed, the only participant of GUN's attack to even make it inside Lava Shelter is E-123 Omega, who asks Shadow for assistance in breaking through to the scientist at the base's core. Alternatively, Shadow can slow the G.U.N. forces down by activating the base's defenses, ensuring that his confrontation with Eggman won't be disturbed by the humans.
No matter which route Shadow takes to his final confrontation with Eggman at the base's core, it ends with Eggman facing Shadow in the Egg Dealer with Omega supporting Shadow during the fight.
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