The game concept revolves around a combination of platform and puzzle elements, challenging Mario to find keys, reach a locked door, and rescue mini-Marios.

Mario vs. Donkey Kong was a return to the earlier arcade-style games that incorporated many elements from the Game Boy version. While its style was that of other games, the Rare design for Donkey Kong carried over. Donkey Kong, originally a villain, returns to this role in the game: wanting a Mini Mario clockwork toy, he finds that they are sold out at a local toy store. Enraged, he terrifies the Toads at the factory and steals the toys. This sets up the game’s plot, where Mario chases Donkey Kong until he can take the Mini Marios back from Donkey Kong.