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 Geoffrey 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.
Sally, Dylan and Hamlin manage to get communication lines working when Charles and the Robians greet them. Sally is enthusiastic to have their cooperation, but Rudyard argues that life will never be the same for Robians. Charles reassures Sally, explaining that some people will need time to adjust.
On the outskirts of Robotropolis, Sonic throws a fit over the fact that his Uncle Chuck never told him his parents were dead when they had been hiding in Robotropolis all along. Tails defends Charles, saying that his parents were a kind of casualty and that Chuck probably
didn't want Sonic to feel the same pain Sally felt when she knew her father was trapped in the Zone of Silence. Sonic finds himself in better spirits and they head back to the city. Later that evening, Sally tells NICOLE that it would be better rebuilding somewhere else than trying to fix Robotropolis. Geoffrey arrives and tries to comfort Sally, but Sally tells him that her heart belongs to Sonic. Just then, Sonic arrives and punches Geoffrey. They get into a fight and have to be sprayed with a fire hose to stop. Sally demands that they apologize to each other, but they quietly agree that their fight isn't over.
Sally calls her father, who demands that she continue to pretend to lead while he makes the decisions for the kingdom. Sally questions her duty, but her father demands that she follow his instructions. Sally tells NICOLE that keeping this a secret isn't right, but NICOLE reminds her that she's kept secrets from her friends before and that she has to fulfill her duties. The next morning, Sally stumbles upon the Robians making the decision to start their own colony in Robotropolis. Rudyard explains that he's already heard Mobians making disparaging remarks about Robians. Meanwhile, Rotor sends Snively on a transport to the Devil's Gulag. Trapped in his cell, Snively thinks to himself that the Mobians underestimate him and that, eventually, he'll make his escape.
This is the first issue where Sonic finds out that his parents, Jules and Bernadette are alive.