"I am Shadow the Hedgehog. The Ultimate Life Form born to rule all! With the power of these emeralds, I'm going to conquer the universe. This is who I am!"
The attack on G.U.N. Fortress went as planned. The Black Arms crippled their defenses and pushed into the base with time to spare on their schedule. But as the last Chaos Emerald was in reach, the plan hit an unexpected snag; Shadow. At first, Shadow joined the attack. But as he progressed through the fortress, he silently took out Black Arms troops along the way, the Chaos Emeralds belonged to him and him alone. When he made it to the center of the base, Black Doom caught on to his betrayal.
The alien warlord confronted Shadow and demanded an explanation. The hedgehog dropped his ruse and challenged Black Doom in combat, proclaiming his allegiance to himself alone. With the element of surprise on his side, the fight quickly ended in Shadow's favor. As he stood atop Black Doom's corpse, seven emeralds in hand, Shadow announced his new position as the ruler of the Black Arms and demanded they bow before him. With G.U.N. defeated in the attack, the alien army complied with the Ultimate Life Form's whim.
Though Sonic and the leader of G.U.N. managed to flee in the confusion of Shadow's coup, the President didn't make it. Further resistance on humanity's part would result in failure, especially with Shadow wielding the Chaos Emeralds. This didn't stop some groups from fighting, though. They were quickly dealt with. The rest surrendered as reality set in; Earth belongs to Shadow the Hedgehog. To further facilitate this, Shadow burned down the capitals of every nation on the planet as the Black Arms made their occupation official.
The people of Earth would only wave one flag now; Shadow's.
But it wasn't enough, Shadow craved more power. Combing Black Arms technology with Earth's, he constructed a fleet to venture out into space. With the Black Comet as his flagship, Shadow mobilized his armada and led both the Black Arms and humanity into an era of everlasting conquest. Planets fell before the might of Shadow's forces, his army grew with each world he conquered, the populations of each world were given a choice; assimilate or face the end. Despite the power he amassed, Shadow always craved more. He wouldn't stop until all in the universe submitted to his rule.
Why shouldn't they? He's the Ultimate Life Form after all.