- This issue takes place between Sonic the Hedgehog #39 — #40
After beating Bunnie Rabbot and Knuckles the Echidna, Mecha Sonic proceeds in destroying Knothole Village. Believing Sonic to be a traitor, Sally orders Rotor to bring in the Roboticizer that was used to roboticize part of Bunnie's body. Knuckles awakes in a daze and attacks his friends, thinking that they are enemies. Sally snaps Knuckles out of his dizzy state by kicking him from behind. Sally explains their need for drastic measures and hands him a Neuro-Overrider to let him keep his free will. Now in a stable mind, Knuckles agrees to be roboticized and jumps in the roboticizer.
Meanwhile, Mecha Sonic finds Tails and targets him with the intention of vaporizing him. Inside though, Mecha Sonic begins struggling with himself, knowing that even as a robot slave he can't kill his sidekick. Before an ultimatum is reached, Dr. Robotnik contacts Mecha Sonic, demanding the coordinates needed to find Knothole so he can nuke it. Mecha Sonic still has second thoughts, but he is unable to disobey his master. Right before Mecha Sonic can give Robotnik the numbers to locate Knothole, Mecha Knuckles arrives and attacks Mecha Sonic, destroying the communicator linking him to Robotnik.
The battle between Mecha Sonic and Mecha Knuckles is brutal and seems endless. Eventually Mecha Sonic decides to put a stop to it and brings all his strength into one powerful hit, sending Mecha Knuckles straight towards Robotropolis, where a stockpile of nuclear warheads are waiting to go off. Mecha Knuckles realizes there is no way he can stop himself before the impact, but is not about to go alone. By reversing the polarities of the magnets built into his knuclaws, he manages to pull Mecha Sonic in with him. The two are caught in the explosion, and the Freedom Fighters fear the worst.
In the rubble that was Robotropolis, Robotnik emerges from his secret shelter and finds Mecha Sonic among the ruins, barely alive. Amazed at his creation's survival, Robotnik gloats about his success. Out of the blue, he is head-butted by Mecha Knuckles, who then explains his survival through the use of an older roboticizer unit that did not use cheap foreign parts and how Mecha Sonic pushed himself in front to shield Knuckles and took the brunt of the blast. Robotnik passes out and Mecha Knuckles flies back to the Great Forest with Mecha Sonic.
Knuckles arrives and delivers Mecha Sonic to Sally and the Freedom Fighters, barely making it and in danger of burnout. While Knuckles is changed back into flesh and blood, Rotor tells Sally that Sonic may not be easy to restore, due to the lethal damage done to his body by the explosion. Sally stands near Sonic with tears coming down her eyes, wishing that their was a way she could save him. Suddenly, NICOLE volunteers to restore Sonic herself by synchronizing with the aura protecting his psyche created by his One Billionth Power Ring. Dubious at first, Sally eventually allows NICOLE to try and she succeeds in restoring Sonic back to normal. Sonic gathers his senses and stands up in front of his fellow teammates, but then Knuckles comes in front of Sonic to gloat about his victory. Angered, Sonic tells Knuckles to take a hike, Knuckles does so, leaving Knothole in the care of the Freedom Fighters.
Immediately after, Antoine snaps handcuffs on Sonic and uses NICOLE's wartime protocols to charge Sonic for treason by allowing himself to be roboticized. Before Sonic can explain himself, the other Freedom Fighters realize what Antoine is saying makes sense and Sally orders Sonic to be taken to the Knothole jailhouse for holding until his trial.
Don't Let the Island Hit You on the Way Down!
While the Freedom Fighters defend Mobius from Mecha Sonic, The Chaotix are losing a battle with a group of invaders on the Floating Island. Predator Hawk and Sergeant Simian easily defeat Charmy and Mighty. Simian calls his comrades and tells them that they set off an alarm and to stay on guard. A siren sounds across Angel Island, prompting Vector to tell Espio that something must be up. Espio has made himself invisible to ambush the enemy, but Lightning Lynx lands a sneak attack on him, using his keen senses to sniff him out. Vector is hit from behind by Flying Frog too fast for him to react. The Fearsome Foursome meet together with the unconscious Chaotix.
Simian boasts that the group didn't understand how to use the element of surprise. The Chaotix suddenly jump up and attack the invaders, explaining that they pretended to be unconscious so they could better understand their enemy and work together to defeat them. Mammoth Mogul strikes the Chaotix from behind and explains his history to them. He tells them that he was once the ruler of the entire planet, and that a Chaos Emerald gave him immortality. He also explains to the Chaotix his plan to take the Floating Island's Chaos Emerald, making him more powerful and able to destroy Dr. Robotnik's empire. The Chaotix launch a collective beat-down on Mogul. Realizing he had planned his attack wrong, Mogul uses his staff to summon his ship and escape with the Fearsome Foursome.
Eel of Fortune
P.B. Jellyfish watches a fleeing Octobot and tries to sting him, but Octobot explains that he doesn't want to fight and just wants to get away from "him". P.B. is then ambushed by the boss of the underwater underworld, Eel Capone. Eel's hired mussels brutalize P.B., leaving him in bad shape. Some time later, P.B. is found by the Forty Fathom Freedom Fighters, who have been told by the P.I.A. that Eel Capone was responsible for their friend's injuries. P.B. asks if Big Fluke could help them, but he is busy migrating. Eel Capone and his mussels are attacked by Finja, who came to the aid of the FF. The FF easily recognize Finja as Bottlenose and congratulate him for defeating Eel Capone. In celebration, the FF watch a choral choir, with Eel Capone suffering from their singing.
- This is one of the comics that Mecha Knuckles appears in.