In the River City Zone, Brutus and his army of Trooper Badniks successfully capture a group of civilians. Brutus divides them up into two groups (after destroying a Trooper who questioned his orders), before sending his ship to a pre-programmed location. The rest are to be taken to the Metropolis Zone and to Doctor Robotnik, where they would likely become Badniks. Back at Citadel Robotnik, Robotnik congratulates Brutus, but is not so impressed at the number he brought back. Brutus' excuse is that he is still learning. Later, Grimer has put the finishing touches to a pair of 'portable Brain Scanners', designed to absorb a copy of Sonic the Hedgehog's or his friends' brain patterns and learn their secrets - such as where does Sonic hide or where the Emerald Hill folk are. After commenting that it was a plan worthy of Robotnik himself, Grimer is zapped by Brutus' laser (set to stun) and steals his brain waves, learning how to build Badniks in the process.
As Grimer wakes up, Brutus lies that Grimer fainted from exhaustion. Brutus then travels to the Misery Zone, current home to the other group of prisoners, where he reveals that Robotnik does not know about this plan. The citizens are initially happy, until they learn they're to become Badniks belonging to Brutus himself. As Robotnik discovers from Grimer that Brutus has obtaining portable scanners without informing him first, Brutus greets his newly-constructed army of Badniks. In the Cotton Factory Zone, Johnny Lightfoot learns that the citizens are sheep whose wool is used to make Robotnik's egg-cosys for no pay. He vows to help them, before being confronted by Brutus and his new army.
Johnny starts his fight well, standing up to the oncoming Badniks, but is getting tired. Remembering why he is here, Johnny heads towards the factory with a view to freeing the slaves. As Brutus sings to Johnny's demise, Johnny yells for the sheep to clear the Zone. The following Badniks attempt to kill Johnny, but keep missing, instead hitting the factory and eventually causing to explode, destroying all the Badniks. Johnny has succeeded, but is caught by Brutus himself who uses the mind scanners on him. Johnny is cool about Brutus knowing the identity of Bob Beaky's Travelling Circus, but realises he has been beaten when Brutus sets his sights on the Mushroom Hill Zone, current home to the Emerald Hill Folk.
Brutus reveals how he obtained this information from a clueless Johnny, whilst Robotnik continues to wonder what Brutus is up to. Brutus reveals he plans to turn against Robotnik, becoming the most powerful ruler the planet has seen. However, something happens to Brutus and he fires upon a couple of Troopers, completely destroying them. Realising their boss has "gone mad", the Troopers head to relieve Brutus of his duty but find themslves destroyed too, but not because of Brutus' desire to. Brutus realises it is the mind scanner that has stolen the personality of Johnny - heading back to his ship, he reverses its effects and crushes it so it can never happen again. Unfortunately, he has forgotten Johnny's secrets, so heads back to the Misery Zone where his Badniks continue to wait for his orders...
- Brutus' Badniks are destroyed by the resulting explosion caused by them in the Cotton Factory Zone. However, it would seem that the 'organic batteries' inside the Badniks also perished, caught in the inferno of the building.
- When Brutus stole Grimer's knowledge, he should also have stolen his traits. Perhaps then, this should mean that he would act like Grimer, someone who is totally devoted to Robotnik and his leadership of Mobius.
- This is the last Brutus story before his final appearance in Revolution.