The Freedom Fighters are ecstatic when their deroboticizer’s initial test proves to be successful, as Bunnie gets her normal body back. Sally wishes to wait and see whether or not Bunnie has any side affects, though Sonic refuses to listen to her and he rushes off to Robotropolis in order to rescue Uncle Chuck, as he wishes to try to restore his humanity once and for all.
The Freedom Fighters rescue an individual named Ari who claims to be a Freedom Fighter from a different organization. While the Freedom Fighters’ are skeptical at first, the group decides to help Ari rescue his comrades. However, when Sally intercepts a message that proves Ari’s intentions aren’t pure, she rushes off with Dulcy in an attempt to save Sonic from being sucked into the void.
Dr. Robotnik is away from Robotropolis at the moment, leaving Snively in charge. However, when the Freedom Fighters attempt to exploit the opportunity to rescue some prisoners, Snively hits Sonic with a laser that causes him to lose his memory. Snively decides to convince Sonic that he works for him and that the Freedom Fighters are evil, in which Sonic believes him and he decides to infiltrate Knothole Village in send its coordinates to Snively. It’s up to Sally to convey the message to the rest of the Freedom Fighters before it’s too late.
When the Freedom Fighters fail a mission that causes several members to be captured and roboticized, Sonic and Sally contemplate that it would be so much easier to go back in time to stop Dr. Robotnik before he took over. Despite the fact that the two of them realize that its just wishful thinking on their part, Dulcy expresses that she believes they really can go back in time, so she persuades them to let her take them to a flying island that was thought to be nothing more than a myth.
Dr. Robotnik’s coup has just started and it’s too late for Sonic and Sally to prevent him from ever coming into power. However, when the two of them went back in time they had altered the timeline, in which Dr. Robotnik is planning on roboticizing their child counterparts as well as destroy the Great Forest through the use of a strange gas. If Dr. Robotnik succeeds at either of these tasks, the future will cease to exist and Sonic and Sally will fade away, so the two of them must do their best to fix the past in order to return to the present.
Fed Up With Antoine: When Antoine becomes king of the Nasty Hyenas, he attempts to enjoy himself and live the good life. However, when he discovers that the hyenas actually want to eat him, he has a sudden change of heart.
Ghost Busted: Sonic and Antoine take Tails into the woods in order to give him some training that he’ll need as a Freedom Fighter. However, when Antoine disappears in the middle of the night, Tails starts to believe there’s a monster in the vicinity.
Dr. Robotnik has managed to find Dragonsnest, the ancient home of the dragons, in which he plans to roboticize them in order to add them to his army. To make matters worse, Dulcy has left the Freedom Fighters in an attempt to find Dragonsnest, so Sonic and Sally must head off to rescue the dragons and get Dulcy back before it’s too late.
Sonic is searching around in the Great Unknown when he suddenly gets sucked into the void, though he manages to escape before getting dragged all the way in. However, he finds an artifact on the ground after these strange events and he decides to take it back to Knothole Village to let Sally analyze it. Sonic doesn’t have time to stick around though, as he is summoned by Uncle Chuck who provides Sonic with some troubling news, though when he gets back to Knothole Village, he discovers that Sally and Bunnie are nowhere to be found.
The Odd Couple: Sonic’s house is destroyed in the middle of a blizzard due to Dulcy’s poor landing skills, though since he cannot rebuild his house due to the blizzard, he finds himself forced to live with Antoine for the time being. Sonic makes the most out of the situation and he continues to live as he normally would, though his sloppy and inconsiderate lifestyle soon proves to be too much for Antoine to handle.
Ro-Becca: Antoine is helping Rotor out with one of his latest inventions, though when he inadvertently activates the machine before it was ready, it instantly falls in love with him due to his accent. Antoine does his best to hide from Ro-Becca, though the weather outside soon proves to work towards his disadvantage.
Using King Acorn’s list, the Freedom Fighters head off into the Great Unknown in hopes of reuniting with another Freedom Fighter organization: the Wolf pack. While the Wolf Pack is cautious of their offers to help, the two groups soon find themselves working together when Dr. Robotnik’s activates his test Doomsday Pod, which proves to be quite resistance to most of their attacks.
There is a very powerful artifact in the world that could perform the greatest of goods or the most unspeakable of evils if it were used in certain manners, though due to the risks involved in using such an artifact, they have been hidden away for centuries. However, when Dr. Robotnik discovers the location of half of the artifact, the Freedom Fighters must work together in order to prevent him from acquiring the other. Unfortunately, Sally isn’t old enough to access the document King Acorn stored in Nicole, so the Freedom Fighters must attempt to figure out how to get the data before it’s too late.
Dr. Robotnik has noticed that the Freedom Fighters have always been one step ahead of him, which causes him to wonder if there is a spy amidst his organization. He attempts to set up a trap to find the spy, though the Freedom Fighters intercept a message that reveals what Dr. Robotnik is attempting to do. Antoine heads off to try to warn Uncle Chuck before it’s too late, though when he gets captured by Snively, Sonic must rescue Antoine before he reveals the name of the spy.
The Freedom Fighters are feeling good about their recent string of successes. With all of their groups united and set up across the world, they begin to prepare for their ultimate attack on Dr. Robotnik’s forces. However, when Dr. Robotnik starts his Doomsday Project earlier than expected, the Freedom Fighters soon find themselves hopelessly outnumbered, in which Sonic becomes their only hope to succeed.