Several of the levels in Elite Beat Agents are thematically similar to those found in Osu! Tatakae! Ouendan; for instance, a level where the agents help a white blood cell named Cap White eliminate a virus inside of an athlete's body shares similarities to a level where the cheer squad (the main characters of Ouendan) must assist super-heroesque medicine as it fights a virus in a violinist's body. In addition, some of the story characters from Osu! Tatakae! Ouendan show up in the stories for Elite Beat Agents. The individual stories are not linked by an overarching narrative, but do pop up in various other stages. For example, two celebrity sisters help a lost dog who called on the agents. In a later stage, the sisters call for help from the agents themselves. In the final two stages, all of the characters in the game reappear, when the agents must face a worldwide threat.

Like Ouendan, the tone of the stories told in Elite Beat Agents is primarily humorous. Although the first few stage scenarios are fairly mundane, such as helping a babysitter control a trio of rowdy children while trying to impress her boyfriend, they progressively become more fantastic. For example, one of the last stages is about a washed-up professional baseball player who battles a fire-breathing golem in a theme park. The one notable difference to this trend in the game is the stage "A Christmas Gift," in which the agents assist a young girl in reuniting with the spirit of her deceased father. This shift in tone is further marked by the game's "clap" gameplay sound effect being replaced with more subtle chimes accompanying the stage song, "You're the Inspiration."