Shortly before Robotnik's takeover, the defenders of the North Pole region had left to visit friends far off. When they returned, they found Robotnik had already conquered their territory. Forced into hiding, the Arctic Freedom Fighters fled into a deep underground cave below Robotropolis. Using some of Robotnik's discarded technology, they were able to create a climate which they could survive in.
When Robotnik created his Weather Annihilator and caused the climate to change, the the Knothole Freedom Fighters were unable to locate Knothole and return home. Seeking shelter in a cave, Sonic the Hedgehog and his friends were nearly captured by SWATbots who were closing in on their location. However, the Arctic Freedom Fighters managed to bring them to a secret location before the SWATbots arrived. Afterwards, when the Knothole Freedom Fighters attempted to destroy the Weather Annihilator, Snively managed to freeze all of them with his ice blaster. However, the Arctic Freedom Fighters soon arrived and freed them. Shortly afterwards Sonic destroyed the Weather Annihilator, and the Arctic Freedom Fighters returned to the arctic.
Some time later, two of the Arctic Freedom Fighters, Sealia and Augustus, tried to help Rotor save his family from Robotnik's mind control. The three managed to sneak into the Walrus' main location, hiding in a trojan-horse. When they emerged, the three began attacking the Snowbots (models similar to SWATbots). However, before Sealia could rewire Robotnik's base to explode, the mind-controlled Walrus horde closed in on them. Outnumbered and not wishing to hurt Rotor's family, Augustus broke the ice between Rotor and the other Walruses, preventing them from getting to the Freedom Fighter and preventing them from carrying out Robotnik's orders. Rotor realized he would have to return another time to break Robotnik's hold over them, and departed.
Long after Robotnik's death The Arctic Freedom Fighters informed Rotor that the hypnosis appeared to have worn off. Rotor had to see for himself, and was at peace until the hypnosis started up again. The Arctic Freedom Fighters had to save Rotor from his totaled submarine, as well as break the bad news that Rotor had already figured out; Robotnik had returned, this time in the form of his alternate universe counterpart Robo Robotnik.
They later participated in the battle against the Xorda.