Shadow the Hedgehog rushes into the city in his search for the Chaos Emeralds after Black Doom appears before him as the Black Arms invade Westopolis. He quickly runs into Sonic the Hedgehog, who asks him to help fight the Black Arms throughout the city, before grabbing the first Chaos Emerald within Westopolis. Doom's Eye appears to him not long after, demanding that Shadow instead kills the GUN Soldiers defending the city.Shadow eventually finds the second Chaos Emerald on his own. An outraged Black Doom shows up in holographic form and reprimands Shadow for disobeying him. Shadow, however, tells him that he no one can tell him what to do and that he is collecting the Chaos Emeralds for his own reasons. This make Black Doom note that Professor Gerald has done more to his memories than he realized. Hearing Gerald's name catches Shadow's attention, but Black Doom sees that Shadow does not remember him. As Shadow tries to question him though, Black Doom has had enough and decides to punish Shadow for his disobedience by teleporting the hedgehog to Glyphic Canyon using Chaos Control.
After obtaining two Chaos Emeralds in Westopolis on his own, Shadow is scolded by Black Doom for his disobedience, and is teleported to Glyphic Canyon using Chaos Control. In the meantime, the Commander learns that Shadow was in Westopolis with the Black Arms, and sends soldiers after him in order to kill him. Back in Glyphic Canyon, Shadow meets Knuckles the Echidna, who is trying to defeat the Black Arms in the area. He later finds Doom's Eye, who tells him that he needs to activate five Temple jewels in order to unleash the power of the Black Arms.
Shadow ignores Knuckles and Doom's Eye and gets the third Chaos Emerald on his own. In the meantime, at the White House, the President receives a phone call that informs him of a report from the Central Information Agency. According to the report, the United Federation's forces have managed to push the Black Arms out of Westopolis and suppress enemy forces in five other cities. The caller also reports that the CIA's mainframe has been compromised, which they suspect the Black Arms are behind. Responding to the call, the President informs them to tell the Commanding Generals that the United Federation will never surrender to terrorists. The President then takes a look at a picture of Sonic and Shadow on his desk and adds that mankind must now defend the peace the two hedgehogs created when they saved the earth, and that they must stand united against the Black Arms. Meanwhile, Shadow goes to Prison Island.
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