The plotline of Bonanza Bros. varies from region to region:

• In the original Japanese version of the game, Mobo & Robo are thieves who work for personal gain. The opening cutscene begins with them watching what appears to be a news report about Badville's tourism being decreased by criminal behavior, and the image of a shadowy figure on television would be used by other localizations to modify the plot.
• In the European version, Mobo & Robo are thieves called upon by the shadowy figure to counter criminal orgnaisations in Badville with their burglary, with a bail out of prison being offered as a reward. This plot is also used in the microcomputer versions of the game published in the UK by US Gold, however in those it is specified that Mobo and Robo are "reformed villains" utilising their sworn-off skills rather than villains working for a benevolent figure.
• In the American version of the game, the plot is dramatically altered. Mobo & Robo are renamed to Mike & Spike, and are changed to be detectives who are simply retrieving pilfered items without any ill intent beyond desiring a reward from the shadowy figure. The scene of the intro where they sneak past a wanted poster is removed. Despite this, the American box art still portrays the Bonanza Bros. as criminals on a wanted poster. No modifications were made to the game for the US release beyond the manual and intro, and thus burglar-related imagery (i.e. bags of loot, nefarious digitized "eh heh heh" cackling, policemen and guard dogs to shoot as enemies) remain intact.

Their character bio in Sonic & Sega All-Stars Racing, despite being a Western-developed title without a Japanese release, uses their original Japanese backstory.

In the Sega Genesis version, Level 9 contains paintings in the background featuring cameo appearances and references to Sega games, including Fantasy Zone, Columns, Super Hang-On, and Altered Beast.