The music video for "Pardon Me" was directed by Steven Murashige and also gained considerable airplay. The video begins with two clones of Boyd, one young and one elderly, at opposite ends of a hallway. As the two approach each other, the more elderly clone begins to regress in age and appearance, while the younger clone begins to grow more elderly, becoming more and more alike as they advance toward each other. When they meet, they pass through each other and continue on in opposite directions. Footage of the band members in white outfits (except for Boyd, who is shirtless) in a red-colored box are also shown, as is footage of the band members in red outfits being surrounded by businessmen and businesswomen.
The song describes a state of confusion, with allusions to spontaneous combustion. Lead singer Brandon Boyd says he was inspired to write the song after making a connection between images of spontaneous combustion in a magazine and "some turmoil in [his] life, both good and bad", namely coming back from a tour to find out that his girlfriend of 7 years had been cheating on him, and that both his grandmother and a close friend of his had died. After seeing a picture in a magazine of a man who had spontaneously combusted, he related the man's problems to his own and was inspired to write the lyric "Pardon me while I burst into flames" on his hand at that spot.
Musically, the song combines fast-paced, ambient verses with prominent DJ scratching and a hard-rocking mid-tempo chorus. However, the acoustic version of the song is also well regarded by fans, and helped the song become a radio hit. Initial radio reception was lukewarm, so Boyd and guitarist Mike Einziger decided to perform the song acoustically at several radio stations that had been playing the song, including KROQ-FM, and this acoustic version grabbed the attention of radio programmers and listeners. An acoustic version of the song was released on the When Incubus Attacks Volume 1 EP.