Sonic the Hedgehog discovers a strange-looking Chaos Emerald lying in the grass of Green Hill Zone which is multi-coloured: the top is white, the upper middle is black, the lower middle is red, and the bottom is green. He grabs it, and sudednly he splits into four versions of himself, each with differing personalities and appearances. Dr. Eggman appears and reveals his plot to make Sonic weaker by making his power split into four different beings who should be unable to work together due to their conflicting personalities (which are all different parts of Sonic himself's personality). Dr. Eggman then teleports them to the Chaotix Realm and shatters the Four Emerald, sending Paladin to the Light Dimension, Asassin to the Shadow Dimension, Barbarian to the Anger Dimension and Scholar to the Puzzle Dimension then heads off to collect the Chaos Emeralds so he can conquer the world.
After finding all 4 cores the sonics are transported to their world... but their world had been transformed into the Nega World and the sonics must find the Four Emerald. After finding the four emerald they are caught by eggman who throws them back in time...
Each of the four Sonic's correspond with one of the colours from the Four Emerald and a different aspect of Sonic's personality.
- Paladin - The leader, he represents Sonic's sense of justice and his conscience. He appears the same as Sonic but his quills point upwards like Super Sonic and his fur is a lighter blue. His eyes are also yellow. He is the colour white from the Four Emerald. His stages revolve around stunts.
- Assassin - The second in command, he represents Sonic's sadness, self doubt, and other emo-like emotions. He wears a black robe and hood, concealing his face, and has red lines across his arms. He is the colour black from the Four Emerald. His stages revolve around fighting.
- Barbarian - Barbarian represents Sonic's anger, hatred, and the way he rushes into situations without thinking about them first. He appears the same as Sonic, but his fur is red and he is more muscly. He is the colour red from the Four Emerald. His stages revolve around speeding.
- Scholar - Scholar represents Sonic's common sense, intelligence, and his cool and collected attitude. He appears the same as Sonic, but his fur is green, he always wears glasses and he carries a book. He is the colour green from the Four Emerald. His stages revolve around puzzles.
Paladin's Story (Light Dimension)
The First Trial
The Second Trial
Assassin's Story (Shadow Dimension)
First Deathly Challenge
Second Deathly Challenge
Barbarian's Story (Anger Dimension)
First Speedy Challenge
Second Speedy Challenge
Scholar's Story (Puzzle Dimension)
First Puzzle Challenge
Second Puzzle Challenge
Final Story (Nega World)
Nega Green Hill Zone
Nega Marble Zone
Nega Spring Yard Zone
Nega Labyrinth Zone
Nega Star Light Zone
Nega Scrap Brain Zone