The game is a 3D platformer, following the trend of recent Sonic games such as Shadow the Hedegog 2: A Twist in Time. Each level has three possible missions — "Hero", "Dark", or "Normal" — that may be completed by the player. Which missions are completed determine the direction of the game's plot progression, a feature referenced by the game's tagline, "Good way or bad way? Anyway!" To defeat the enemies found in the game, Silver can use his psychokinesis and levitation, as well as homing attack and hand-to-hand combat. The plot of the game involves Silver, a mysterious time-traveling hero, attempting to learn about his past and parents, since his life had been ruined by the Ifrit.
Silver can use his pyschokinesis and hand-tohand fighting skills to defeat enemies. Another new feature in the game is the addition of vehicles such as cars that Silver may drive though most of the vehicles are optional. Although Silver can sometimes run faster than the game's vehicles, the vehicles have some capabilities that Silver does not, such as hitting and running over enemies, or traversing a normally impassible acid-covered area. The Sol Emeralds play a major role in this game. They aid Silver's memory, and allow three "Psychic Powers" to be performed after filling up the player's "Hero", "Normal" and "Dark" gauges. "Psychic Control" allows Silver to manipulate time and space, "Psychic Blast" creates an explosion that damages enemies, and "Psychic Mind" allows Silver to temporarily possess an enemy.
There is a multiplayer mode for two players, in which they can play as Silver or bonus characters; Dark, Tela and Alet. It has the same basic mechanics as the single-player mode, but the screen is divided horizontally between players. Players fight in one of four specially designed stages and can attack each other and steal each other's rings until one is defeated. In the story mode, a second player can connect a controller to the second socket and play as Silver's partner for a mission, unless Silver is supposed to follow that character.
Fourteen years before the game takes place, a baby, white hedgehog was born to unknow parents. This baby was named 'Silver the Hedgehog' and possesed the ability to harness the power of the Sol Emeralds. In Sonic Rivals 2, it was thought that he returned to his time and lived a happy life. But he returns in this game with an eagerness to know his past and who is parents were or are. At the beginning of Silver the Hedgehog, which takes place three months after Silver returned to the future, he still knows nothing of his past; his only memories is being carried by an unknown female hedgehog who was running away from another unkown character. The game begins in the city of Underopolis, where the Xorda are invading; its leader, Adrox, speaks to Silver of an old agreement made between Adrox and Silver's parents for Silver to bring him the Sol Emeralds. Stunned that Adrox knew him by name, Silver realizes that he must find the Sol Emeralds to learn the truth about his past.
The game progresses through several more levels, each of which involves Silver completing missions and learning more about his past. He can choose to take the side of the Adrox who wants the Sol Emeralds for themselves, Doctor Eggman Nega, who wants to build his own empire and defeat the Adrox, the GUN army, who want to keep the world safe from the Adrox and Doctor Eggman Nega, Blaze and co. who want to hide the Sol Emeralds and destroy the Adrox or take no side and choose to seek the Emeralds for himself. The missions completed determine which of the ten possible endings will be reached. The endings occur after defeating the one of the game's final bosses, when Silver collects all the Sol Emeralds. Possible endings range from Silver planning to destroy the Adrox to planning to destroy the planet.
Silver the Hedgehog/Psychic Silver (Main Character)
Adrox the Xord (Dark Supporting Character)
Blaze the Cat (Hero Supporting Character)
Dr Eggman Nega (Dark Supporting Character)
Sonic the Hedgehog (Hero Supporting Character and Multiplayer Character)
Big the Cat (Hero Supporting Character and Multiplayer Character)
Tails the Fox (Hero Supporting Character and Multiplayer Character)
Marine the Raccoon (Hero Supporting Character)
Espio the Chameleon (Hero Supporting Character)
Ifritian Priest (Dark Supporting Character)
Knuckles the Echidna (Hero Supporting Character)
Metal 'Met' Sonic (Other Character)
Shadow the Hedgehog (Other Character)
Melissa the Hedgehog (Other Character)
Shadow (who was still alive in the future due to being immortal)and Melissa (a psychic hedgehog) gave birth to Silver, but were forced to a deal with Adrox. If Silver joined the Xorda then he will live, but if not... Shadow and Melissa tried to save Silver, but Shadow vanished in the process and Melissa was killed. In the Final Ending, Silver lays a silver rose on Melissa's grave and vowed to find Shadow, his father.