After Shadow either destroys most of Central City, makes his way through The Doom, or decimates the Eggman Fleet, GUN's flying battleships are evacuating from Central City. There, in the White House, the Commander arrives with two of his men and urges the President to evacuate to a more fortified position to protect themselves from the advancing Black Arms, which the President reluctantly agrees to after some encouraging words from the Commander. Shadow and Black Doom stand outside the building as they watch the President escape towards GUN's flying battleship holding position overhead. Black Doom orders Shadow to follow the President. Shadow then skates off towards the battleship that the President's escape pod is going to as it begins to depart.
Immediately upon boarding the battleship, Shadow runs into Tails, who asks for Shadow's help in protecting the President's shuttle from the Black Arms' boarding parties by defeating all the aliens. If Shadow chooses to side with Black Doom instead, he must destroy the shuttle, which is being conveyed on a monorail track through the ship, before it reaches the safety of a secure hangar in the ship and is unable to be pursued further. Alternatively, Shadow can simply pursue the Chaos Emerald located in the ship.
After Shadow either helps Dr. Eggman dispose of the GUN troops in Iron Jungle, or claims the fifth Chaos Emerald in the ARK or Air Fleet for himself, Black Doom telepathically informs him that GUN soldiers have been raiding the Black Comet, and orders him to exterminate them. Meanwhile, the comet itself is seen passing by the Space Colony ARK.
Upon infiltrating the Black Comet, Shadow comes across Doom's Eye, who has him eliminate the invading GUN troops. Shortly after, however, he finds Knuckles, who wants him to go with him to the core of black comet and claim the Chaos Emerald the Black Arms have stolen.
Shadow fights off the GUN soldiers as has been ordered, and gets the sixth Chaos Emerald. Soon after, he is confronted by Sonic and the Commander, who is piloting the unfinished Diablon mech. He, however, manages to defeat them and gets the final Emerald in the aftermath. When interrogated by a beaten Sonic, the black hedgehog reveals that he, being the Ultimate Life Form created to protect Black Doom, will use the gems to transform earth into the "dark empire".
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