Role as a Non-Playable Character
Commander Kahn appears to be responsible for locating the various emergencies that the Elite Beat Agents deal with and dispatching the agents themselves. At the beginning of each mission Kahn can be seen watching the character in peril on a giant computer screen, before turning around in his chair, pointing into the air and shouting "Agents are go!!" with particular emphasis on the word "Go" (with the exception of the 'A Christmas Gift' mission where he simply remains staring silently at the screen and the 'No More Music!? The Last Hope!!' mission where he is not seen at the beginning at all). At the end of a mission, if all stages of the song have been completed successfully Kahn will spin around in his chair and shout "Yeah!!", displaying a thumbs up, however if one or more stages of the song were failed, he will simply appear looking straight forward with a serious look on his face and his hands clasped below his chin. Kahn also appears in the background of the 'New Bonus Stage Unlocked Screen', standing over the camera and giving a thumbs up.
Role as a Playable Character
Commander Kahn can be unlocked as a playable character by completing every song in the game on every difficulty. When Kahn is in play, the difficulty of the game is set to 'Hard Rock'. The character Mr. X is also unlockable for use in the multiplayer mode and is unlocked at the same time as the 'Hard Rock' difficulty. This character seems to simply be Commander Kahn with the head of a cat, and this is further evidenced by the fact that once Kahn is unlocked as a playable character he will replace Mr. X.
Notably, he dances with the female animations, rather than the male ones.
- At the beginning of the mission 'Survive! Celebrity Lives and Desert Isles!!' Kahn can be seen wearing a red Hawaiian shirt instead of his normal suit.
- At the beginning of the mission 'The Last Laugh! Just a Peanut Matter!!' Kahn can be seen with a can of 'Sarcastic Nuts & Nuts' on his desk, to the right of him. Due to a glitch this can will also disappear before the game cuts away from Kahn.