Six Degrees of Inner Turbulence is a type of concept album wherein the five songs which comprise the first disc explore different themes of lifetime struggle, such as alcoholism, loss of faith, self-isolation, sanctity of life and death. The title track, a 42-minute track occupying the second disc, separated into eight parts - explores the stories of six individuals suffering from various mental illnesses.

Particularly represented are bipolar and post-traumatic stress disorder, schizophrenia, post-partum depression, autism and dissociative personality disorder. Furthermore, the title of the album may also allude to the fact that each song on the album could be seen as a different form of inner turbulence, with the six tracks making another reference to the six degrees, along with the apparent reference to the six degrees of separation.

The musical styles of each section of the title track are direct reflections of the band's large variety of influences. Classical, folk, jazz and metal styles are present within the track.

Influences for the album's writing and recording include Metallica's Master of Puppets, Radiohead's OK Computer (and also a Radiohead bootleg Portnoy brought in), Pantera's Vulgar Display of Power and the song "Mouth for War", Megadeth's Rust in Peace, U2's Achtung Baby, Tool's Ænima, Nine Inch Nails' The Downward Spiral, Soundgarden's Superunknown, Alice in Chains' Dirt, Kevin Gilbert's Thud, King's X's Faith Hope Love and Galactic Cowboys' Space in Your Face, Béla Bartók, Rage Against the Machine's The Battle of Los Angeles, and Maria Tipo's Chopin Nocturnes.