On his Knuckles' World Tour of Mobius, Knuckles has found himself on the Great Mobian Prarie, still dragging along the chest of Floating Island documents. He pauses for a moment to rest, but is interrupted by an apparent earthquake, which is quickly revealed to be a stampede by a herd of Apterix. Above the stampede, riding Pterodactyls, are a number of wranglers, one of whom, Chito, is in search of someone, who he believes has been trampled to death by the herd. The man in question, Rooster, emerges from behind a rock, alive but unsure as to what caused the stampede. Suddenly, Knuckles appears nearby, throwing off the boulder he used as cover from the Apterix. Chito is quick to accuse Knuckles of starting the stampede and ignoring the Echidna's protests and Rooster's attempted suggestions, zaps him with a cattle prod. As Knuckles lies weakened, Chito reveals that there have been several 'accidents' with the herd lately, and convinces Rooster to take Knuckles to nearby Backwater, so the sheriff can deal with him, and so Rooster can get his herd safely to Metropolis City, the rest of the team leading the Apterix in Rooster and Chito's absence.
In Backwater City, Knuckles has been imprisoned by Deputy Krouch in a brand new steel cell. Chito and Rooster explain the situation to the Deputy, who decides to keep Knuckles in until the Sheriff returns. Just then, Boss Krouch, the city mayor and Deputy's father visits to give Knuckles the once over. Apparently relieved that Rooster's alive, but angered at Rooster's suspicion, he leaves, Chito leaving shortly after, food on his mind. Knuckles and Rooster talk, discussing the Apterix meat market. Rooster acknowledges that if he were to have an accident, Boss Krouch would be the only supplier, and decides that he and Knuckles will wait for the Sheriff and let him work out what's going on. That night, Chito and a frustrated Krouch are in the saloon, where Chito reveals that he and Krouch are working together, he started the stampede and he's worried about what will happen to him when the Sheriff realises Knuckles is innocent. Krouch assures Chito that Knuckles is being taken care of, and at that moment, a lynch mob storms the jail and drags Knuckles out for a public hanging, apparently told that Knuckles killed Rooster. Before Knuckles can hang however, his noose is shot through by the Sheriff who orders everyone home. Knuckles gets to his feet saying he has a few complaints to report....
The next day, Krouch's son is fired from his position as Deputy, and Knuckles is offered the position. The Sheriff sees Rooster off as he goes to rejoin his team with the Apterix herd, while Knuckles, having accepted the Deputy role, is doing a little reconnaissance in the saloon, having been told by the Sheriff that he shouldn't leave until they know who's trying to kill Rooster. The barman offers Knuckles a drink, but the echidna refuses, finding Chito on his mind. As if on cue, Chito appears behind Knuckles, and when Knuckles punches Chito's gun out of his hand, it unfortunately lands in another patron's beer, sparking a tavern brawl. Knuckles fights a few of the brawlers off and flings Chito out into the street where he reveals that Krouch has left town and plans to try and kill Rooster himself.
That night, Rooster and his men are resting up and eating, while being observed from above by Boss Krouch and his cronies. As he's about to make his move, 'Chito' appears in the shadows. After a brief chat, Knuckles steps out of the shadows, removing his Chito disguise, with the Sheriff behind him, having heard Krouch's 'confession' of his trying to wipe out Rooster, straight from the horse's mouth. Krouch makes a run for it, and Knuckles follows, the Sheriff staying to deal with Krouch's men. Knuckles backs Krouch onto the edge of a cliff, where Krouch reveals his trump card: A vial containing a chemical compound which, to the Apterix, smells like their most feared predator, but 100 times more potent. He threatens to throw the vial into the herd, but falls from the cliff. He is unharmed, and makes plans to kill Knuckles there and then, but has accidentally splashed the compound on himself. Krouch is swiftly trampled to death by the rampaging Apterix, and Rooster returns the chest to Knuckles, noticing that it looks rather heavy, and offering some assistance to the Echidna... As dawn breaks, Knuckles continues his journey home, now riding one of Rooster's Pterodactyls.
- The strip derives its name from the classic Western film, The Good, The Bad and The Ugly.
- Originally, Knuckles was drawn with the noose around his neck in the lynch mob scene. The scene was edited in reprints of the story, so the rope was tied around his fists.
- There is a typo on the first page of Part 2, with Rooster saying he'd "better bring the varmint it", rather than "in".