Sonic Chronicles: The Dark Brotherhood’s Associate Producer Dorian Kieken has said in an interview that the Sonic Chronicles 2 story is already being written.
During his SavyGamer Podcast interview he talks about designing the game, music and story. Then goes on to mention that developer BioWare are already writing the story for Sonic Chronicles 2 as part of their future DS titles. Sonicstadium transcribes that Dorian explains they already have a lot of different scenarios for what will happen next and they have a good idea of where they want to go with the game.