At the end of Shadow the Hedgehog, Black Doom is defeated and thrown into the Black Comet, which is subsequently destroyed. However, it is later revealed that Black Doom survived and is now plotting revenge against Shadow and the rest of the world.
In the sequel game, Sonic the Hedgehog (2006), Black Doom returns as the main antagonist. He leads an invasion of the human world and attempts to use the Chaos Emeralds to power a weapon called the Eclipse Cannon. Shadow and his friends are able to stop Black Doom and destroy the Eclipse Cannon, but Black Doom himself escapes.
Black Doom's ultimate fate is unknown, but it is likely that he was killed when the Black Comet was destroyed. However, he could also have survived and could potentially return in a future game.