As the second of three rhythm games developed by iNiS specifically for the DS, it is the follow-up and international counterpart to Osu!

Similar to Ouendan, the player taps and drags on indicated locations on the touch screen of the DS in time to the rhythm of the music to score points, while the upper screen shows comic-style scenes of the fictional "Elite Beat Agents" cheering on others in tough situations through their dance moves.

The main characters of Elite Beat Agents are well-trained spy members of a fictional government agency responsible for helping those in need.

The person's degree of success depends on the accuracy of the Agents' dance moves, as demonstrated by multiple endings for each story.

Although the first few stage scenarios are fairly mundane, such as helping a babysitter control a trio of rowdy children while trying to ask a potential boyfriend to go steady, they progressively become more fantastic, with higher stakes.

Another plot aspect taken from Ouendan includes a "sad" level more than halfway through the campaign that is based on a slower, mellow song, titled "A Christmas Gift", in which the agents assist a young girl in reuniting with the spirit of her deceased father.

The main campaign culminates in a climatic planetary crisis in which the Agents, along with all humanity and the people they helped in prior levels, facing off against an alien invasion staged by the Rhombulans (a portmanteau of rhombus and the Romulan race from the Star Trek franchise), who abhor music and use a petrification ray to enforce a ban on it.

However, unlike Ouendan, this final scenario is divided into two levels, with the first level showing the Agents rallying prisoners to stage a riot against the aliens before sacrificing themselves to the ray, leading up to the second and ultimate final level where the people devastated by their sacrifice gather resolve and determination to reverse their petrification and help organize an epic musical counterattack against the aliens, triumphantly unleashing a blast of spirit energy to the sky to obliterate the Rhombulan mothership.

Music heard in the game is performed by cover artists, and in most cases, adjusted for length to be three minutes long.

Success is monitored by the "Elite-O-Meter", a health gauge at the top of the touch screen that is constantly draining at a rate based on the selected difficulty level, out of four total.

The first three levels of Breezin' difficulty, the easiest one, feature an on-screen indicator to highlight the order in which the markers must be hit.

If the Elite-O-Meter is in the yellow when the player reaches one of these breaks, the story will depict the person in need making significant progress towards his or her goal.

If at least one section is passed, but not all of them, then the story will have the average ending, where the main character succeeds with moderate success.

The Agent Rank is a special title such as "Soldier of Song" or "King of the Beat" that will change as the player's cumulative high score reaches specific milestones.

During the song, each player can fill a star meter by completing Elite Beats; when the star meter is full, the screens of the opposing players will shake for a few moments, and the on-screen markers will be reduced in size for a short time, making them more difficult to hit.

Ouendan, Nintendo and iNiS began discussing the possibility of officially localizing the game beyond Japan.

The first concepts were of a trio of dancers styled after the Village People called the Disco Rangers; this was changed to a trio of government agents, using distinctly Western references such as the Ghostbusters, Blues Brothers, Men in Black and Austin Powers series for inspiration.

[5] Yano conceived the latter character, who has no Ouendan equivalent, while trying to determine a good motivation for the Agents' service.

[6] When it came to choosing songs for the game's setlist, which was planned to comprise twenty songs as opposed to just fifteen in Ouendan, Yano looked for ones that he thought would be ideal to blast in a "college frat party", while making sure that the setlist drew upon multiple genres and time periods.

[8] According to E3 trailer footage and UI programmer Robert Ota Dieterich, "Livin' La Vida Loca" was originally going to be used for the game's second level, before being replaced with Sum41's "Makes No Difference".

Upon release, Elite Beat Agents was critically acclaimed, receiving an average score of 87.7% on GameRankings.

Then-president of Nintendo of America Reggie Fils-Aimé has stated that while sales were strong, he was disappointed that they were not better, having expected 300,000 copies sold in light of critical acclaim.

[39] Despite the game never being officially released in Japan, Agents drew the interest of import gamers in the country,[40] just like how Ouendan was enjoyed outside of it.

One month after the game's first release in North America, Fils-Aime himself, disappointed with initial sales, expressed hope that Agents could get a sequel and become a franchise,[26] but ultimately nothing came of it.