The Syndicate was a terrorist group led by Doctor Zachary. From their flying fortress, the Death Carrier, they planned to use the Chaos Siphon to set off a chain reaction that would have destroyed Mobius, but were foiled by Sonic using a Chaos Tap. They are also responsible for stealing the Chaos Emeralds and using them to destroy the Special Zone. The group has since disbanded.
- Doctor Zachary : The group's de facto leader. Captured by Knuckles and brought back to the Floating Island after being betrayed by Vichama.
- Doctor Robotnik: Insane former ruler of Mobius. Mute and driven by a murderous need to personally kill Sonic. Disappeared in the explosion of the Death Carrier, but has since returned, partly controlling the New Robotnik Empire.
- Shadow the Hedgehog: The ultimate life form created by the Drakons. Totally apathetic and devoted to Robotnik, who taught him all he knew as Doctor Kintobor. Died in the explosion of the Death Carrier while teleporting Robotnik to safety.
- Vichama : The God of Death, initially in the form of a muscle-bound echidna from the ancient past. When the Syndicate's plan backfired, he used the Chaos Emeralds to escape his echidna body, taking on a spectral form. Later returned to the Floating Island and revealed his true form, only to be killed by Knuckles and his own undead army.
- Rouge the Bat: Treasure hunter and double agent, secretly working for the Drakon Empire. Disappeared as soon as the Chaos Siphon began to backfire. Currently being pursued by Dunzi and the Household Keepers.