got to work doing damage control in Station Square, Dr. Eggman searched for a means to use this new phenomenon to his advantage, in which he learned of Professor Dillon Pickle and his research of the Gaia Manuscripts. The doctor immediately kidnapped the professor and his research, along with Uncle Chuck.[5] The Freedom Fighters were able to save the two from a speeding Bullet Train, though leaving the research behind for Eggman to acquire. Both hero and villain learned of Dark Gaia, an ancient creature which resided in the earth's core whom, due to the Super Genesis Wave's effects, was prematurely awoken during its sleep cycle, and its energy has began to seep through the cracks and manifest into Dark Gaia Creatures,[6] who would ravage the world duringthe same time, the heroes would aid those affected unfortunately by the world crisis.[15]

Knuckles' quest would eventually coincided with the Chaotix' newest assignment set by Sally to find a Chaos Emerald. In a stroke of luck, the amnesiac Light Gaia (whom Charmy rechristened "Chip") was in possession of the emerald in question. The group were able to rescue Chip and secure the emerald from the hands of the Hooligans.[16][16][17]

Throughout the Freedom Fighters' travels, Sonic began exhibiting odd feral behavior when under stress due to the Dark Gaia Energy that Sonic had accidentally inhaled before.[3][5][6][14] Despite Chuck's insistence, Sonic brushed off his worries.[6] Sonic's attempts to bottle up his feral moments came to a head during a mission to retrieve a Chaos Emerald from the Soumerca Egg Army base.