Living in the wreckage of a rusty old airplane on the shimmering shores of South Island, Sonic the Hedgehog and his buddy Miles "Tails" Prower have not a care in the world. The president of Planet Freedom urgently summons the duo, but trouble is afoot when Sonic and Tails instead find the good-for-nothing Dr. Eggman lounging about his office as if it were his own.

While Sonic would prefer to scramble Eggman and move on with his day, the doctor claims not to have new plans for world domination. He instead pleads for help: the generator powering Eggman's home city of Eggmanland has been hijacked and overloaded by a mysterious menace. If left unattended, it will explode, taking both Eggman and Sonic's homes with it.

Reluctantly agreeing on the off chance Eggman is telling the truth, Sonic and Tails set out into the abyss—where an unknown yet uncannily familiar enemy lies in wait.