Sonic is turned into a Merhog by one of Tails' inventions and begins a new life in the ocean. While exploring, he finds a Merhog prince named Shadow, whose family adopts Sonic as their son. One day, the two run into someone named Mephiles, who has plans of his own for the two Merhogs.
Sonic the Hedgehog has been hiding something from his past: he was abused as a child at the orphanage he was in. When Shadow finds out, he is determined to help him. As Sonic is diagnosed with schizophrenia, things take a turn for the worse...and Sonic will learn what it means to be insane.
Tails has created a new invention that turned Sonic into an artificial intelligence in order to see what Eggman is up to. They soon get a visit from Shadow, who tells them that the Black Arms are approaching and are ready for war, and eventually discover that the Black Arms have teamed up with another alien species called the Covenant, and are searching for something called Halo.
When Shadow and Sonic are killed while coming home from work, their son Shadic goes back in time to stop it from happening but ends up going too far back to when Sonic and Shadow first met. Now he has to get back to his own time before the future is changed forever, or he will never be born.
Sonic has just been crowned King of Camelot and is ruling well. He gets a surprise after his son shows up, who has been wondering where he's been. Shadic must go on an adventure and help defend the kingdom from the evil Mordred, who has set his sights on the king's destruction.
Knuckles the Echidna has a vision from the Master Emerald and goes back in time to Transylvania. When he gets there, however, he meets Dracula and the other vampires, who are in control of the world, and forms a resistance in hopes on combating the evil vampires. But little does he know that they have only just begun.
Shadow and Sonic are on a run when they encounter Dr. Eggman. The evil scientist hits them with a laser that causes them to transform into each other, causing them to live each other's lives. But along the way, they discover something about themselves that will have their lives change forever.