After the events of 'Sonic the Hedgehog 2', G.U.N.'s deadly project yet, by the name of "Project Shadow", breaks out of their facility and breaks loose, along with another project of G.U.N.'s, "Project Rouge". Dr. Ivo Robotnik, or Eggman, has returned from the hospital due to losing to Sonic again. When Dr. Eggman and Stone encounter Shadow and Rouge, Eggman sees this as an opportunity to frame Sonic as Shadow's "faker", to use Shadow and Rouge to finally defeat Sonic. Now Sonic, Tails and Knuckles (as well as a new friend) have to defeat Eggman, Shadow and Rouge, along with a new creation by the name of OMEGA, before Shadow becomes the ultimate threat he was never meant to be.
