The comic starts out with Sonic and the rest of the Freedom Fighters journeying into the reclaimed Mobotropolis, after defeating Dr. Ivo Robotnik. They enter Dr. Robotnik's main control room, and hear a noise. This turns out to be a Dynamac, which is then shorted out by Bunnie Rabbot when it steps in a puddle and Bunnie uses a electrical pipe to fry its circuits. Rotor Walrus pulls back a curtain to reveal Snively, who then tries to run away only to be caught by Geoffery St. John. Sonic the Hedgehog and Tails head off on their own, and Tails notices a SWATbot walk by, and thinks he's outnumbered. Sonic comes to help Tails, only to see that they're just putting supplies on a conveyor belt. Uncle Chuck goes down a sewer pipe, and tells some Robians that were given their free will back from the effects of the Ultimate Annihilator, all saying they'd prefer to stay underground than go back up. Sonic hears a cry for help, and finds Arlo the Armadillo and Penelope Platypus in a room, Arlo trapped under a heap of rock. Sonic tries to free Arlo but fails, until Rudyard appears and frees Arlo from the rock. All the other Robians come with Uncle Chuck, two of them confronting Sonic, telling them they are his parents. Sonic runs away in a rage, saying Uncle Chuck should've told him that his parents were alive.
This is the first issue where Sonic finds out that his parents, Jules and Bernadette are alive.