Thirteenth Step

The band's writing process was very different from the band's first album, Mer de Noms. With the first album, a majority of the album had been already written and recorded over a long period of time by guitarist Billy Howerdel, before a band had even been assembled.[6] He had recorded it with a female vocalist in mind, but upon Tool vocalist Maynard James Keenan hearing it and offering to sing for the material, the content was then quickly finalized upon adding Keenan's vocals and re-recording the drums with band member Josh Freese.[6] With beginning the second album, the band found themselves starting fresh, without any material to start with, with the exception of the track "Vanishing", which originally was intended to be on the band's first album, but Howerdel could not find the song file in the studio, having accidentally named it "test".[6] Upon finally recovering the track in 2001, it was only slightly altered for its final release, to better match the eventual sound of Thirteenth Step.[6] The title "Vanishing" was a tongue in cheek allusion to the fact that the song itself had gone missing.[7]

Writing for the album started while Keenan was still touring with his other band, Tool, in support of their 2001 album Lateralus.[8] Howerdel would write most of the music, while Keenan would write most of the lyrics.[9] As such, Howerdel would send work in progress instrumental he would create, and Keenan would write lyrics in between shows, a process they found to be efficient, but ultimately more difficult to balance than they initially expected.[8] Keenan's work with Tool was not the only thing delaying work on the album, as progress was also hampered by other lineup changes, including guitarist Troy Van Leeuwen leaving to be a member of Queens of the Stone Age, and bassist Paz Lenchantin leaving to be a member of Zwan, leading to their contributions to the album being limited to only a few tracks.[8] Lenchantin would be replaced by Marilyn Manson bassist Jeordie White, while Van Leeuwen would be replaced by Danny Lohner on the album and later James Iha for touring purposes, as Iha did not actually perform on the album.[10]

Once touring for Tool was over with, Keenan returned to the studio to work in person with the rest of the band on the album. The sessions were, as such, marked with far more collaboration, especially between Howerdel and Keenan, now that Howerdel knew who his vocalist was, and what types of ideas he'd support.[6] At times, this would cause a creative struggle between the two as well; since Keenan was involved with some of Howerdel's music writing this time around, he would sometimes give more input in the music, with the two sometimes wanting to move in opposite directions.[8] Keenan, in particular, wanted to move away from the general hard rock sound of Mer de Noms, feeling that taking that approach again would be "redundant".[8] He instead pushed for a softer sound, focusing more on atmospherics and ambience.[10] Conversely, Howerdel preferred the heavier compositions written while waiting for Keenan to return from Tool.[11] White, relatively new to the band, often played the role of mediator between the two, being able to offer an outsider's perspective of the situation.[11]

Danny Lohner played a large part of the productions of the track "The Noose", whereas "The Package" was a full-band collaboration that started with Howerdel playing the song's basic guitar riff in front of everyone.[6]

Thirteenth Step is a concept album about the different aspects and perspectives of addiction, and the recovery from it.[13] The album's title itself is a reference to the 12 step program of Alcoholics Anonymous.[10] Lead vocalist and primary lyricist of the band Maynard James Keenan explained the concept on the band's DVD Amotion, stating:

"The songs on Thirteenth Step for the most part are about the various processes of addiction, behavioral addictions, chemical addictions, and each song is kind of sung from a different perspective. I have a lot of friends who've gone through a lot of these situations. Some of the songs are sung from the perspective of the actual drug, from the perspective of someone who has realized that they have an issue or a problem, also from the perspective of a person who realizes that if they don't do something they're going to die, a song from the perspective of a person who is in denial about a loved one, dying right before their eyes. And in the case of "The Outsider", it's sung from the perspective of a person who doesn't understand at all what their friend is going through, what their loved one is going through, and they think that it's more like a sprained ankle; they can just kind of walk it off."[14]

Keenan, not having struggled with addiction first-hand, drew from experiencing it happen to others around him, such as Layne Staley, the lead singer of Alice in Chains, who died in 2002 due to drug addiction.[12] The song "The Package" is from the perspective of an addict, desperate for more, while "Blue" is from the perspective of someone having a difficult time dealing with the aftermath of an overdose.[8]

"The Nurse Who Loved Me" is a cover of the song by Failure, originally featured on the 1996 album Fantastic Planet.