The Rebel Underground was a resistance group opposed to the dictatorship of Dr. Ivo Robotnik. It was formed in the later years of the war against Robotnik and led by Geoffrey St. John. For some time this organization operated alone, until Geoffrey made contact with the Knothole Freedom Fighters. Afterwords, the two groups worked together on a number of occasions, and after Robotnik's defeat the group was reorganized into a new Royal Secret Service, with Geoffrey St. John eventually becoming the only member of the original group still working as a field agent.
During the Great War, it was brought to the attention of King Max by General Armand D'Coolette that an underground rebel movement might be needed if the kingdom was ever taken over by an enemy within. Because of his foresight, Armand began to train his son Antoine as a soldier in preparation for a day such as that. Sadly, Armand was Roboticized and became Robotnik's Sub-Boss, the High Sheriff, before the Underground was ever established, leading to Geoffrey's claim at having formed it followed by Antoine's outrage at having his family's honor stolen and his father's memory insulted. (StH: #46)
In their first encounter, Geoffrey was carrying out a solo mission until he ran into Sally Acorn at one of the energy substations for Robotropolis' defense grid. They both thought each other was involved with Dr. Robotnik's forces until they came under attack by SWATbots. After escaping, Geoffrey decided to let Sally in on Robotnik's Auto Automaton scheme and went to Sally's campsite with her own robot duplicate, where her trainees were waiting. Meanwhile, the real Sally placed herself in the duplicate's stasis pod to avoid suspicion. Geoffrey then joined Sally and her trainees on their mission to destroy another energy substation and were attacked by Orb Bots, though both were scrapped.
Their next mission was to destroy another substation which could only be reached with hang-gliders. Arlo was shot down in the approach and broke his leg, so Penelope stayed to help him. Shortly after the others left, the rest of the Rebel Underground appeared and rescued them both, putting a cast on Arlo's leg, and disappeared with them before the others came back from dealing with the substation and its Octo-Pod guard. Before dawn the next morning, Geoffrey woke up the real Sally, who led Hamlin and Dylan to infiltrate another one of Robotnik's bases.
After reaching the facility's core, they found Geoffrey and Robotnik side by side. Hamlin accused him of being a traitor and attacked him until Sally threatened to hit him with red paint. Robotnik revealed that the substations were a ruse to test the robot duplicates created in the factory in which they were standing. This was supposed to assess how well they could impersonate real key figures in the Freedom Fighters. Believing the operation to be a complete success, Robotnik decided to roboticize what he thought was the real Sally. However, it was actually the fake which was placed in the Roboticizer and the subsequent Roboticization process caused the unit to explode. Robotnik realized he been betrayed by none other than Geoffrey and set his Stealth 'Bots on all of them.
At the last moment, Geoffrey called in the rest of the Rebel Underground, and Lt. Smiley and Commander Fleming emerged from underground with Arlo and Penelope, beginning to attack. After that, Robotnik activated a built-in bomb which obliterated the factory, though everyone escaped safely before it detonated. In the aftermath, Sally explained everything and made her trainees official Freedom Fighters. She then asked St. John to join the Freedom Fighters, but he denied, saying that he was the leader of his team and could not abandon them. The two kissed and Sally left for Knothole, while St. John went off on his next mission. (PSM: #1, #2, #3)
Hijack and DYNAMAC
The Rebel Underground reappeared on the Robotnik Express while attempting to stop the train and destroy Robotnik's newest weapon, the DYNAMAC, before it reached West Robotropolis. For this mission Geoffrey brought along Jean-Claude and Dolph, but was soon reunited with Sally who jumped on board back in Robotropolis as both their teams were doing the same mission. Sonic the Hedgehog encountered Geoffrey here for the first time and was instantly jealous of both of them acting so close. They were soon attacked by the DYNAMAC, which self-activated as the train's guard and turned its attention to its main priority: Sonic. Sonic tried to distract it while Geoffrey and Sally attempted to defeat it, but Sally was soon captured and so were that the other Freedom Fighters in the Freedom Fighter Special after that. Sonic grabbed Nicole who pinpointed where the DYNAMAC's weakness was, allowing Sonic to input Nicole's virus while Geoffrey distracted it in-turn. Once vulnerable, Jean-Claude and Dolph finished it off with a long-range firearm. After the Freedom Fighters got control of the Express, Sally and Geoffrey kissed each other another farewell with Sonic bearing witness to it. With that, the Rebel Underground departed on another mission, leaving Sally to return to Knothole with her own team. (StH: #31)
After the murder of Sally for which Sonic was found guilty (but was really framed due to the manipulation Hershey Cat by Drago Wolf of the Wolf Pack), he escaped custody thanks to a SWATbot ambush while en-route to the Devil's Gulag. The Rebel Underground were then tasked with hunting down Sonic and bring him to "justice," dead or alive. Lead once again by Geoffrey, they used Tasmanian Devils to track the scent of Sonic and sometime later had him cornered on top of a waterfall at the end of a cave network. Geoffrey engaged Sonic in hand-to-hand combat, overcome with grief for Sonic killing his only love (though Sonic retorted that St. John only loved himself). After Sonic escaped and flew away on Dulcy, they followed him to the Floating Island thanks to a tracking chip in his cuffs. Arriving via aircraft, Geoffrey attempted to recruit Knuckles and Espio who already caught Sonic before Dulcy managed to speak up and proclaim his innocence. Realizing that Robotnik was attempting to divide them from within, Geoffrey had Sonic's shackles undone and flew them (including Knuckles) back to Knothole just in time to liberate their home from the SWATbot and Combot forces that overran it in their absence. (StH: #48, #49, #50, SSS: #6)