The Chao have disappeared and Sonic the Hedgehog and Miles "Tails" Prower immediately get on the case to find them. It turns out that Eggman Nega (once again masquerading as Dr. Eggman) has stolen the Chao and concealed them inside a haunted mansion. His plan is to feed them to an inter-dimensional beast called the "Ifrit" who needs to eat them to become invincible. After that, he plans to release the Ifrit into the world in order to destroy it. However, to open the portal to the Ifrit's world, the seven Chaos Emeralds are required. Eggman Nega secretly hires Rouge the Bat to collect the Chaos Emeralds. The Master Emerald has also gone missing (again) and Knuckles the Echidna teams up with Rouge to find it.