In ELITE BEAT AGENTS, players tap and rhythmically drag the DS stylus on the touch-sensitive screen. The zany premise is that there's a secret agency called the Elite Beat Agents (EBA), which exist to help the downtrodden. Think Men in Black meets John Travolta's Saturday Night Fever. When the agency detects a plea for help, three agents appear and, with the players' help, dance their way to solving the problem.

Each of the stories is presented on the top screen in the form of a manga-style comic strip. Each episode has three possible endings, which relate to the amount of energy produced in terms of points. The most common move involves tapping a sequence of numbered dots corresponding to the beat of the music. How well you execute these moves affects how you fill your Elite-o-Meter -- if the meter runs out, the good-deed-doing is over, and the EBA fails at their mission.