Tails is passing through the Casino Night Zone, planning to assist Sonic the Hedgehog in the Metropolis Zone. However, his attention is diverted when he hears cries of help from below. Visitors to the Zone are being persued by Troopers, ordered to exterminate all non-robotic life forms by Commander Brutus. Tails comes to the rescue by beheading a Trooper (despite one rabbit preferring it if Sonic had saved him). A skunk begs Tails to help rid the Zone of Brutus' troopers and Tails agrees, although busy. Nearby, old foe Fleabyte the Bounty Hunter spots the fox and plans to capture Tails, cash him in for the reward and make up for his lousy luck in the casino. With Tails distracted, Fleabyte casts a net over him and captures him. However, his glee is quickly dissolved when Troopers accost him. Thinking he is exempt from Brutus' persecution by having a robotic arm, he is sorely mistaken as he gets thrown into a cell with Tails.
The hero curses his luck, stuck in a cell waiting for extermination with a flea-bitten Fleabyte. Tails questions his fellow inmate, wondering if his robotic arm does anything useful like fire laser beams. The cat says no, only using it sometimes to pick locks. Tails, not believing Fleabyte's stupidity, urges him to pick this lock and get them out of the cell. As the pair burst out of the back of a lorry, the Troopers open fire, willing to exterminate their targets there and then. Tails is at home battling the Badnik forces, but Fleabyte runs, wishing he had his guns with him. Tails saves him by emptying a pot of syrup in front of the chasing Troopers, sending them careering into a pinball machine.
With Fleabyte saved, the bounty hunter shows his "gratitude" by attempting to capture Tais with his net, again. The fox is ready this time, catching the net and wrapping Fleabyte up with his own weapon. With the cat left to dangle from a lamppost, the Zone Leader thanks Tails for his good deeds and asks him to stay a bit longer to protect them from more Trooper attacks. Believing that Sonic could cope without him for a few days, Tails stays put, Sonic himself having taught him that "the safety of the citizens comes first."
- This story marks Fleabyte's last appearance. He does, however, make a cameo appearance in The Syndicate; his sighting in an asylum suggests he has somehow gone insane.
- Fleabyte Returns is the second in a three-part series, chronicling Tails' reaction to the rise of Brutus. Although he meets the troubling Spider-Moth, Tails never does make it to help Sonic fight Brutus' Revolution.
- In the first panel, a rollercoaster seems to come off the tracks, a rather thrilling addition to a theme park.