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The Secret Freedom Fighters were a team of covert agents formed by Harvey Who and sponsored by Elias Acorn. Their primary mission focused on taking back the Republic of Acorn from Ixis Naugus without taking actions that would directly oppose the will of its people and their secondary mission was to prevent the events that lead to Silver's future. The team's agents, each of whom had been assigned a codename for mission usage, consisted of Elias Acorn (King), Silver the Hedgehog (Ace), Shard (Jack), Lyco (Queen of Hearts), Leeta (Queen of Diamonds), and Larry Lynx (Joker). They also had a list of allies which include Sir Charles Hedgehog acting as an informant, and Lupe Wolf being a talent scout for them. They operated out of Secret HQ, a hidden bunker built by NICOLE in an undisclosed location within New Mobotropolis.
When Ixis Naugus made a claim for the crown, he carefully manipulated public opinion to his favour. To avoid conflict, King Elias Acorn stepped down; however, he secretly approached Harvey Who, seeking help to regain control of the government without putting the public in danger. While Harvey was reluctant at first, he eventually agreed to help when Elias proved his determination. Harvey took up the task of finding appropriate candidates for the team. He approached Sir Charles Hedgehog and the exiled Nicole for their assistance, and began recruiting. The first recruit would be Silver the Hedgehog, followed by Shard and Larry Lynx. Leeta and Lyco of the Wolf Pack were the last to join, coming in answer to a summons sent by Harvey. After two of the team succeeded in collecting Elias from Feral Forest where he had relocated, the entire team would secretly aid Team Freedom in defending New Mobotropolis from Dr. Eggman's forces under Team Metal (StH: 233, 235, 237, 238, 239, 240; SU: 42)
Tomb of Vale
Upon learning from from Sir Charles that Geoffrey was bound for Soumerca on Naugus's orders, Director Who dispatched a team to learn the reason behind this. Operatives Ace (Silver), Joker (Larry), and Jack (Shard) followed St. John to Windy Valley, and stuck a tracker on his unattended Extreme Gear once they arrived. They then went underground through a variety of traps designed for Ixis Wizards, and eventually discovered they had entered the tomb of Ixis Vale, finding fresh tracks left by St.John. In the team's attempt to pursue and trap him, Geoffrey managed to escape and caused the tomb to cave in with an explosion. However, Ace used his powers to keep the rubble from crushing them, while Jack started to drill an escape route. In the meantime, Geoffrey fled the area with remains he had stolen from the tomb, unaware of the tracker on his board. (SU: #41)
While the team that was sent after Geoffrey faced their difficulties, Agents King (Elias), Queen of Hearts (Leeta), and Queen of Diamonds (Lyco) were dispatched to investigate Naugus' activity in New Mobotropolis itself. Following him into the crater created by the destruction of Castle Acorn, the trio discovered an underground tunnel leading to Naugus' Ritual Chamber, a mysterious room he had shaped beneath the city. After some friction between Elias as leader and Leeta and Lyco as subordinates, the group briefly split up as Elias set a charge at the tunnel entrance to ensure their escape. Undergoing a hideous transformation due to the influence of Agunus, Nusgau, and Suguna, Naugus became aware of their presence and attempted to destroy them, reshaping the tunnel network and attacking them with his magic. The three were thought eliminated after being hit with a tornado blast that knocked them into the depths of the crater.(SU: #42)
The trio returning from pursuit of Geoffrey reunited with their teammates at the bottom of the crater, comparing notes and determining that Naugus was apparently preparing to unleash some sort of spell. Elias determined that in order to get the information needed to stop Naugus, they would have to interrogate Geoffrey, but the team instead decided to approach the Skunk peacefully at Silver's suggestion. Silver approached Geoffrey, apparently alone, and asked for his help, to which the Skunk revealed Naugus' plan to enslave the Council of Acorn with a spell. After Geoffrey departed, refusing Silver's offer to help them stop his insane master, the rest of the team emerged from concealment, having been ready to capture Geoffrey if necessary. Their enemy's plan revealed, the group prepared itself for a showdown with the dark wizard.(SU: #43)
While Larry Lynx "used" his bad luck abilities to prevent the Council from entering a locked Military HQ, the rest of the team went after Naugus directly. Elias planted explosives on the walls of the ritual chamber, whilst Naugus was engaged by Silver and Shard. Leeta and Lyco engaged Geoffrey, who was in possession of Naugus' Chaos Emerald wand. After a pitched battle, Shard destroyed Ixis Vale's remains and disrupted the spell, Elias finishing the job by detonating the explosives. The team then made their getaway, Shard smashing through a crystal barrier erected by Naugus to enable their escape. Returning to Secret HQ, the group parted briefly, some going out and observing certain citizens in secret while Silver spoke with Harvey, who revealed that he had identified Silver's traitor. (SU: #44)
Shard would later be dispatched to locate and observe Team Fighters, and caught up to them in Albion, where he aided them against the Krudzu Hybrid Hydra after it took control of Metal Knuckles. After the Krudzu was defeated, Shard brought its last remaining sprig back to New Mobotropolis for analysis. With the permission of Team Fighters, he also placed a tracker on the Tornado, which was used by Silver to locate the group in the Northern Tundra. Shard also engaged in a solo mission in battling the latest version of Metal Sonic, which resulted in the other robot's destruction and Shard suffering tremendous damage. (StH: #245, #246, SU: #50)
- The uniforms worn by the Secret Freedom Fighters seem to be based on the "Leather" and "Race" character skins of Sonic Rivals and Sonic Rivals 2 respectively. Silver's uniform is, in fact, his "Leather"\"Race" skin from those games.
- Each of the field operatives uses a call sign based on a playing card. This setup has been joked about both in the comic itself and in an Off Panel of the Secret Freedom story arc. In the case of the comic, Geoffrey was amused by Elias' codename of "King", which obviously referred to the title he had been forced to surrender to Naugus. In the Off Panel, Harvey jokingly remarked that his decision to name the agents after playing cards was because he wanted the team "playing with a stacked deck."
- Due to the lawsuit that lead to Ken Penders's additions to the comic being jettisoned, Silver the Hedgehog is the only confirmed member of the team who can return, with Shard's status left in question.