There are 10 chapters in Sonic Chronicles the Dark Brotherhood. The chapters are called: Chapter 01: Hostile Reception Chapter 02: The Search for Knuckles Chapter 03: Egghunt Chapter 04: A Wolf in the Shadows Chapter 05: Battle for Angel Island Chapter 06: Black Hole Sun Chapter 07: Quest for the Chaos Emeralds Chapter 08: Sector Scylla Chapter 09: Sector Charybdis Chapter 10: Citadel Showdown
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After you fix the elevator fly right.
Oh, Amy's Dexter? He's not real. Amy just made him up to make Sonic jealous. at least that's what everyone on the planet thinks. SEGA could be showing him in a future game, Sonic Chronicles the Dark Brotherhood did leave off with Eggman ruling Mobius, "Dexter" could be alive even after that.
You beat Imperator Ix up on Angel Island and Shade realizes she was being used. She betrays her entire clan(and I believe she and Knuckles have a crush on each other!)
The Dark Brotherhood Sanctuary is located in the Cheydinhal East Gate.