Several years ago, Earth was a single planet until a cataclysmic event split it in two, sending them into two worlds (Sonic's and the humans'). After being transported to Earth by the seven Chaos Emeralds while rescuing Cream from Doctor Eggman's clutches, Sonic the Hedgehog and his friends meet Chris Thorndyke, a young human boy who lets them stay at his house. Despite their initial conflicts with the police, Sonic and his friends are hailed as heroes.

However, as Sonic and his friends were transported to Earth, the two worlds start to remerge, cancelling out their respective time lines and freeze time itself forcing Sonic and friends to return home. Six months later, a new villain, Dark Oak, attempts to get the Chaos Emeralds from Sonic, but Sonic scatters them across the galaxy to prevent Dark Oak from using their power. Meanwhile, six years having passed in the human world, Chris uses a portal to travel to Sonic's world, where only six months had passed, but ends up in the form of a twelve-year-old. During their reunion, Dark Oak and his Metarex army attacks and steal the "Planet Egg" from Sonic's planet. Without the Egg, all the life on the planet goes away. Sonic and his friends venture into space to retrieve the Chaos Emeralds with Dr. Eggman following soon afterwards with his ship: The Crimson Egg.