The game is set on Northern Island, one of the few islands Robotnik hasn't tried to take over yet.. It revolves around the titular heroes Sonic the Hedgehog and Miles 'Tails' Prower, who try to stop Dr. Ivo 'Eggman' Robotnik from succeeding in his plans. The whole game is set in 4 main zones (see the "Stages" tab) and the player is set to have the main game finished in 30 min (or 3 in-game days) or else he fails.

One sunny day at noon, our hero, Sonic the Hedgehog, is taking a nap on the shore of Northern Island, when he was awoken by a floating sheet of paper, landing on him. It is a letter from his arch-nemisis, Doctor Ivo 'Eggman' Robotnik, in which he claims to have created a weapon of mass destruction, capable of burning down the whole planet and the only way for Sonic to 'stop' this weapon was to collect and bring all of the 7 Chaos Emeralds, ancient artifacts of near-infinite power, directly to Robotnik before 3 days pass. If Sonic failed to do so, Robotnik would launch his weapon, destroying the entire planet, and build his empire from the ashes. Thus begins a new adventure for our heroes...