Sonic the Hedgehog and the Freedom Fighters are away from the Emerald Hill Zone, but life still isn't dull. Shorty the Squirrel is having an altercation with another Emerald Hill folk member, a bird who believes that Doctor Robotnik is a good guy. Hopper, Shorty's rabbit friend thinks he'll soon change his mind, as the Zone suddenly comes under attack from a Trooper squadron. The Robotnik sympathiser is the first to be thrown in a prison cell, making the ideal Badnik. One by one, the rest of the village is rounded up, but Shorty manages to escape. Wondering how he is going to save his friends, Shorty stows away on the ship and follows his friends into a Badnik Processing Plant. Before Grimer can turn the animals into new Badniks, Shorty bursts out of a ventilation shaft and damages a compu