1 year after the final battle with Dr Robotnik, Sonic is travelling the world, when he recieves a message from Tails, who later tells him Knuckles has been taken prisoner by the mysterious Marauders, who have also stolen the Chaos Emeralds. Upon gathering a few friends together and rescuing Knuckles, the gang enter an uneasy alliance with none other than Robotnik, and hunt the Marauders down, travelling from Metropolis Zone to the Floating Island, to the Marauders' otherworldly home, the Twilight Cage, and back again.
Sonic Chronicles has not yet had an adaptation in Sonic the Comic Online, but some elements from the comic can be seen within the game. Specifically, Robotnik refers himself as Robotnik, and not the 'Eggman' persona which he has used since Sonic Adventure 2; through the player's dialogue selections, Sonic can be portrayed as a snotty, arrogant jerk as depicted within the comic, the game has a twist ending which bears a striking similarity to a key moment in Sonic the Comic's continuity, Imperator Ix, as a white-furred Echidna, bears a resemblance to Doctor Zachary (though some schools of thought compare him to Archie's Dr Finitevus), and STC characters Sonic, Tails, Knuckles, Robotnik, Amy, Rouge, Big the Cat, Vector the Crocodile, Shadow and the G.U.N. are present, albeit in their Sega guises.
A sequel is apparently in the writing stages, though next to nothing is known about it yet.