Originally, Bruce intended for Skunkworks to be the debut album of a band by the same name. However, the label would not publish the record under any other name than Bruce Dickinson. The album moved even further away from the progressive sound of his former band Iron Maiden into an alternative rock sound similar to bands such as Soundgarden. However, the support tour for the album was the first time Dickinson included a song from his former band, a slightly reworked version of "The Prisoner." Many of the songs lyrics are about science and technology. The band didn't last and for his next solo project, Accident of Birth, he teamed up again with guitarist Roy Z (from Balls to Picasso). The album was produced by Jack Endino, best known for producing Nirvana's first album. The album name refers to the code name for the military testing program.
In 2005, Skunkworks was re-released and the 2005 extended version included songs performed live, such as "Inertia", "Faith", "Innerspace", "The Prisoner" and other previously unreleased songs.