Johnny Lightfoot has met up with a rat in Metropolis Zone, who gives him valuable information, for a price, regarding Robotnik's next big move: Transporting a new secret weapon through the Gum Tree Zone in two days' time. Johnny rushes off to relay the information to the other Freedom Fighters, unaware that Robotnik himself has been watching the events from the shadows. Two days later, the Freedom Fighters are searching for the platoon of Troopers with the weapon, to no success, until Shortfuse's sensors pick them up. Impatient, and keen to show off to Tails, Shorty attacks, and the rest of the gang quickly join in, making short work of the Troopers, who don't put up much of a fight. Before the Freedom Fighters can open the crate and check out the weapon, a robot bursts out, declaring himself as Vermin the Cybernik. Johnny recognises his voice as belonging to the rat informant, proving that the heroes have walked right into a trap. Shortfuse tries to talk to Vermin, thinking they may have some common ground, but Vermin knocks him aside, stating that he wanted to become a Cybernik and is stronger than Shortfuse.
The Cyberniks begin to clash, and Shortfuse's blaster is shown to be weaker by far than Vermin's lasers. When Tails tries to attack, he is literally swatted aside, but he manages to buy enough time for Shortfuse to recover and return to the battle. With his tail, Vermin injects a computer virus into Shorty's systems so his armour can't function properly. Johnny tries to join the fray, but Vermin's laser shatters his staff. The Cybernik is only driven away when Amy steps in and shoots one of the gum tree sacs above him, the acidic juice being corrosive to metal. With Vermin returning to Robotnik for repairs, the gang turn their attention to the damaged Shortfuse, who requests to be taken to a workshop in Emerald Hill Zone. In the workshop, which belongs to Tekno the Canary, Shorty needs a few days to have the virus drained out of his system. Amy, Tails and Johnny are fully prepared to deal with Robotnik on their own for a while, and Shortfuse vows that the next time he and Vermin meet, he'll be ready.