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The Phantoms were created with the Phantom Ruby in order to conquer the world and having unlimited troops. At some point, Sonic the Hedgehog faced Metal Sonic's Phantom while the real one was being upgraded into Neo Metal Sonic, which was completed too late: The Resistance defeated the Eggman Empire and the Phantoms vanished alongside Eggman. (StH: #7)
The Phantoms are based on the Replicas, which appear in Sonic Forces.