Whilst in pursuit of Dr.Eggman, Sonic is sucked into a portal and teleported into a new world engulfed in darkness and paralysed in motion. Taken a-back from his unexpected teleportaion, he meets a green raposa named 'Lenny' who was unconscious; suffering a hard blow to the head. Letting his curiosity get the better of him, Sonic asks Lenny what had happened to the planet, and learns that this dark/sinister looking world is the future.
However, to make matters worse, back in Sonic's timeline, a mysterious character is stealing the chaos emeralds for an unknown purpose. One that only Sonic's friends...