
Black Doom has two new associates for him, namely the Bull's Eye and the Golden Eye, who help instruct Shadow at times while he's busy commanding his troops.
Blaze, Silver, and Infinite are established characters from later games that now appear in this one. Black Doom tells more truth than anyone else, but throws lies into the equation to keep Shadow firmly on his side. Eggman neglects telling Shadow he's anything but one of his rogue androids, leaving him to discover his own answers. Sonic's friends tell Shadow some of his past but can't hint to all of it, with most of his answers coming from Rouge. The correct answers are found on a specific route, but the player can believe what they want to believe. The game rarely relies on details established in previous cutscenes and avoids contradictions when possible, leaving the player to piece together Shadow's past for themselves. He is fully brainwashed by Black Doom and plans to destroy all humans on the Dark Route. He fully believes he's a Shadow Android and plans to take the original's place as an anti-hero on the Neutral route.
He regains his memory and joins Sonic and friends to beat Black Doom on the Hero route. Shadow's purpose is finalized on the 8th stage on every route, marking the point where he can't turn back. All of these stages and their associated bosses (Devil Doom, Deviled Egg, Devil Diablon respectively) can be beaten after defeating Black Doom, Egg Dealer, and Devil Diablon respectively. The Last Way, as a stage, has been renamed to The Right Way, with the Dark counterpart named The Wrong Way and the Neutral counterpart named The Only Way. The "Last Story" feature is reworked into the ending of the Hero path, with identical counterparts now existing for the Neutral and Dark paths as well. It is only necessary to defeat Devil Doom, Deviled Egg, and Devil Diablon once each to beat the game. By clearing a certain amount of missions on other routes, what Shadow says in the ending when he gets all Chaos Emeralds does slightly differ, although all of his evil quotes are brushed to the Dark path and all of his noble quotes are brushed to the Hero path.
This streamlines the game significantly, making plotlines easier to follow.
There are only three different endings in the 2025 remake, namely the Hero, Neutral, and Dark endings, which are respectively earned by defeating Devil Doom, Deviled Egg, and Devil Diablon.