Shadow begins the game with incomplete memories while the Black Arms invade Earth. Black Doom claims a connection to Shadow's past and demands the seven Chaos Emeralds. The branching missions let the player temporarily align Shadow with heroes, villains, or neither side while different routes reveal fragments of his history.
Every normal Story Mode run starts in Westopolis and lasts six stages before a final boss. Completing a Dark, Normal, or Hero mission changes the next stage where that choice exists. The complete graph contains 326 valid story sequences. Shadorux's 326 Route Explorer now follows the actual stage graph rather than placeholder branches.
The branching main story contains 22 stages, from Westopolis through the five possible Stage 6 destinations: GUN Fortress, Black Comet, Lava Shelter, Cosmic Fall, and Final Haunt. See the complete level and route map for every transition.
The five final stages each support two ending routes, producing ten normal endings. Unlocking every normal ending is separate from filling every one of the 326 Library paths.
Last Story and The Last Way
After all ten normal endings are completed, Last Story becomes available. It resolves the game's central conflict with Black Doom and includes the separate final stage The Last Way before the true final confrontation.