The main characters of Elite Beat Agents are members of a fictional government agency responsible for helping those in need. When someone facing a crisis reaches their breaking point and cries out for help, Commander Kahn dispatches the agents to help them succeed. The agents never assist the person directly, but encourage the person through their dancing, motivating the people they assist to overcome various obstacles. The person's degree of success depends on the accuracy of the Agents' dance moves, as demonstrated by multiple endings for each story.
Like Ouendan, the tone of the stories told in Agents is primarily humorous. The individual stories are not linked by an overarching narrative; though some characters take part in multiple stories, there are unique protagonists for each song. 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. For example, one of the last stages is about a washed-up professional baseball player who rescues one of his young fans from, and subsequently battles with using baseball equipment and techniques, 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".
Also in contrast, the final levels in the game involve most of the characters previously helped by the Elite Beat Agents joining together to help eradicate a music-hating race of aliens, the Rhombulans (a portmanteau of rhombus and Romulan), that have invaded Earth. When the Agents are seemingly turned to stone while shielding the rest of the humans, the crowd's combined determination allows them to break free and defeat the remaining Rhombulan troops. A blast of spirit energy is released from the crowd, destroying the aliens' leader and saving the planet.
Several of the levels in Agents are thematically similar to those found in Ouendan; for instance, a level taking place inside the human body, and a tearjerker level. In addition, some of the story characters from Ouendan have cameo appearances in Agents. In the final two stages, as in Ouendan, all of the characters in the game reappear.
The fundamental aspects of gameplay are unchanged from Ouendan to Agents. The stages of Agents are presented in a comic book fashion. After the introduction to a character and their problem, the agents are deployed and the action begins. The play mechanics involve performing one of three actions with the stylus in various combinations.
- Hit Markers - Operated by tapping numbered circles.
- Phrase Markers - Operated by tapping and holding the stylus on a ball within a circle while following it along a path.
- Spin Markers - Operated by spinning the stylus around the on-screen disc until bars on both sides light up.
To successfully perform each action one must complete it as a timed circle converges on each main circle. The timing follows the rhythm of the music. The Hit and Phrase markers must be hit in numbered sequence. The markers are arranged in 'tracks' which range from one to about fifteen markers in length. Success is monitored by the "Elite-O-Meter", a gauge at the top of the touch screen that is constantly draining at a rate based on the difficulty level. Successful actions, such as tapping the Hit Markers in sync with the music, will keep the gauge filled, while missing a marker will partially deplete the gauge. If the meter empties completely, the stage ends prematurely in failure. The first three levels of Breezin' mode feature an on-screen indicator to highlight the order in which the markers must be hit.
Each stage is divided into multiple gameplay sections separated by story sequences, the specific number of which varying by stage. 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 it is in the red, the scene will instead depict the person encountering a setback. In between breaks, during the gameplay, the top screen shows the person attempting to accomplish what they need to do at that time. The scene depicted changes every beat, or when the markers switch color, depending on the player's progress. If the player scores an "Elite Beat" by scoring 300 points on each marker in a single beat, then the person makes a lot of progress very enthusiastically. If the player scores a "Beat" (no score lower than 100, but not all 300), the person will be shown making average progress on their goal. However, if the player does not score a special beat bonus at all by scoring a 50 on a marker or missing it entirely, the person on the top screen will encounter difficulties and setbacks. The player will receive bonuses to the final grade and unlock artwork for completing a stage with positive outcomes at all stage breaks.
Each stage has three possible endings for its story. The ending depends on the number of gameplay sections passed. If all gameplay sections are passed the story will have the best ending, with the main character succeeding in its challenge. 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. If all sections are failed, however, the story will have the worst outcome,where the main character finishes his or her endeavor but still fails.
High scores are acquired by achieving combos, or stringing together a series of successful actions. The longer the player is able to maintain a combo, the greater the multiplier applied to each successful action. Should the player miss a marker completely, the multiplier will stop and the player must start a new one. The game keeps track of individual stage high scores for all difficulty levels, as well as a cumulative high score that affects the player's "Agent Rank." 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. Elite Beat Agents features three bonus stages that are unlocked when three such ranks are achieved.
The player's performance in each stage is rated by a letter grade, with "D" being the lowest possible rank and S being the highest. To achieve an S-rank, at least 90% of all beats must be 300, another 9% must be at least 100, and no more than 1% may be 50. The player must end with a "Perfect", obtained by missing no beats throughout the entire song. However, it is possible to break a combo by missing a dot on a Phrase Marker track and still get an S-rank. Due to the nature of the game's scoring mechanic, it is possible to achieve a new high score in a stage while simultaneously earning a lower grade than the previous high score performance, although this is somewhat rare.
A few additional features have been introduced to Agents from the gameplay in Ouendan. Primarily, these include the ability to reveal more statistics about a player's performance when they complete a song; the ability to save their performance as "ghost" data that they can later use in a "Vs. Ghost" multiplayer mode; the ability to review the last few moments of a failed performance, and the ability to skip the musical introductions to stages.
Up to four players can compete against each other using the wireless capabilities of the Nintendo DS using one or more copies of the game with 2-4 Nintendo DS consoles. The same song list is used, but the stage is set using one of five predetermined, competition-based scenarios.
Only songs that the "host" player has completed are available for play. Each player attempts to perform the song in the same manner as the single player mode. There is no Elite-O-Meter, but instead, the cumulative performance of each player is tracked during the game. At the normal break points for the song, the scene depicts which player is ahead, though it is possible for both players to be tied at this point. 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. The winner is the player with the best cumulative performance at the end of the song.
When utilizing single-card multiplayer, only five songs are available on "Cruisin'" and "Breezin'" difficulties. When all players have a copy of the game, all of the songs and difficulty levels become available, but each scenario is still assigned to a certain song.
This mode can also be played by a single player against a saved replay for any song.
There is also a cooperative mode, in which players take turns to play. Each user must have a copy of the game to do this. Each song uses the same scenarios as the single player game, but only the stages the host has completed in single player are available. Both players share a single Elite-O-Meter, so if one person fails, the game ends for both players. The players take turns playing certain segments of the song, as well as Spin Markers. When it is not the player's turn to play, the markers are grayed out.
All of the tracks that appear in Elite Beat Agents are cover versions.
- Steriogram - Walkie Talkie Man (by Jason Paige)
- Sum 41 - Makes No Difference (by Vinn Lombardo)
- Avril Lavigne - Sk8er Boi (by Angela Michael)
- Freddie Mercury/Queen - I Was Born to Love You (by Paul Vician)
- Stray Cats - Rock This Town (by Mark Latham)
- Deep Purple - Highway Star (by Kaleb James)
- Village People - Y.M.C.A. (by TC Moses)
- Earth, Wind and Fire - September (by TC Moses)
- Jamiroquai - Canned Heat (by Jason Paige)
- Madonna - Material Girl (by Melissa Garber)
- Ashlee Simpson - La La (by Laura Jane)
- Chicago - You're the Inspiration (by Julian Miranda)
- David Bowie - Let's Dance (by Delaney Wolff)
- Good Charlotte - The Anthem (by Kevin Ridel)
- Hoobastank - Without a Fight (by Kevin Ridel)
- The Rolling Stones - Jumpin' Jack Flash (by Billy Fogarty)
The following three songs are unlockable within the course of the game by achieving cumulative high scores across all difficulty levels and stages. As certain high score totals are reached, the player will move up in rank, and by achieving certain ranks, a bonus stage and song is unlocked. If cleared on a lower difficulty, these bonus stages become normal stages on higher difficulties. In the order in which they are unlocked, they are:
- Cher - Believe (by Lynn Rose)
- The Jackson 5 - ABC (by TC Moses and Brittany Kertesz)
- Destiny's Child - Survivor (by April Harmony)