The recording 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 sixth song—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.
"Blind Faith" features lyrics written by James LaBrie about questioning religious belief. It is the second longest song for which LaBrie has contributed lyrics to date, the longest being "Sacrificed Sons" from Octavarium. It was also the first time he had written lyrics for more than one song on an album. The next time would also be on Octavarium.
In the song "Misunderstood", John Petrucci wrote and played the guitar solo, and then reversed it. He then learned how to play this reversed version, and after recording it, reversed it once more. This resulted in a solo like the original but with a unique twist to the way the notes sounded. His use of such a technique was predated by George Harrison, on the Beatles song "I'm Only Sleeping".
"The Great Debate" is intended to be a non-partisan song dealing with the topic of stem-cell research. It was originally titled "Conflict at Ground Zero" based on the lyrics in the chorus but was changed at the last minute due to the 9/11 terrorist attack on New York City. Producers John Petrucci and Mike Portnoy were actually in a Manhattan studio conducting final mixes of the album on the day in question and made the change when all of the news reports started to refer to the site as "Ground Zero."
Lyrics for the song "Disappear" were written by James LaBrie about the subject of death; it was originally titled "Move On".
The sixth song "Six Degrees of Inner Turbulence", which makes up the entire second CD, is the longest song Dream Theater have recorded to date. While recording, they wanted to keep the song at 20 minutes, but more and more ideas came which resulted in the length doubling. Realizing that they would have to cut "Disappear" and "Misunderstood" to keep the album at one CD, their record label was now open for the idea of a double album, something the band had previously been denied when recording Falling into Infinity for former label EastWest.
The last chord of "Six Degrees of Inner Turbulence" is used to open "As I Am" on the next album Train of Thought, continuing a chain which ended with Octavarium.