In an issue of CMJ New Music Report dated May 2000, it was announced the band had signed to Vagrant, due to the success of Through Being Cool (1999). While on tour, in March 2000, the band got into a van accident that almost ended the band's career. The van accident was somewhat of an inspiration for the band's songwriting.
The band played on a few Warped Tour dates before heading into the studio. The band worked with producer Rob Schnapf.
"As Your Ghost Takes Flight" is about a friend's heroin addiction.
At the time of the recording, Saves the Day consisted of Chris Conley, Dave Soloway, Ted Alexander, Eben D'Amico and Bryan Newman and was produced by Rob Schnapf who previously produced Elliott Smith and Beck. The album was a shift from the band's previous power chord-based sound and featured more intricate guitar work and arrangements.
Stay What You Are was released in July 2001 on Vagrant, selling 15,000 copies in the first week.[nb 1]
The band gained some exposure with the single "At Your Funeral", which the video featured a creative way of motion control, similar to Requiem for a Dream. The band also released the single "Freakish", with the video featuring Muppet-esque puppets. In April 2002. Stay What You Are reached number 100 on the Billboard 200 albums chart and is the band's best selling album selling over 300,000 copies in the U.S. In the years since its release Stay What You Are is widely regarded as a classic and a highly influential piece of music for the emo and pop punk genres.