Inspired by the audience response to Dream Theater's heavier songs while on tour, Train of Thought is widely considered their heaviest album to date. The album was written in three weeks. It was engineered by Doug Oberkircher and mixed by Kevin Shirley.There are some connections to previous and following albums of the band:
The album has seven songs, while its predecessor (Six Degrees of Inner Turbulence) has six and its successor (Octavarium) has eight.
The first song "As I Am" starts with the ending synth/orchestral chord of Six Degrees of Inner Turbulence and the ending piano note (F) of "In the Name of God" is the first note of Octavarium's "The Root of All Evil".
"This Dying Soul" continues Mike Portnoy's Alcoholics Anonymous suite, started with "The Glass Prison" on Six Degrees of Inner Turbulence and later continued with Octavarium's "The Root of All Evil" and Systematic Chaos "Repentance". The songs share some of the lyrics and melodies.
The Chant/Hymn at the end of "In the Name of God" (from 12:56 onwards, coming from the right-side speaker) is the American civil war hymn "Battle Hymn of the Republic".
"Honor Thy Father" was written about Mike Portnoy's stepfather. When asked about what inspired him to write that song, he stated in an IRC chat: "I'm not very good at writing love songs, so I decided to write a HATE song!!!"
Between 05:51 and 06:07 of the song "In the Name of God", there was a hidden composition buried beneath the far louder sounds of the song itself which lay undiscovered for over a year and a half. The band did not tell anyone that a hidden "nugget" (as it became known amongst Dream Theater fans) was present in the song, and only when Mike Portnoy mentioned it in his Mike Portnoy: Live at Budokan Drum-Cam DVD over a year later did someone find it. The Mike Portnoy message board was rife with fans scouring the song looking for what it might be, until a fan going by the pseudonymous name "DarrylRevok" mentioned that from 05:51 to 06:07 there appeared to be morse code audible, which Nick Bogovich (user handle "Bogie") isolated and discovered that when translated to English, the phrase "eat my ass and balls" (a Mike Portnoy catchphrase) was the result.
The bridge of "In the Name of God" contains references to several noted cult leaders, including David Koresh, Marshall Applewhite, and Jim Jones.
Stream of Consciousness is the longest Dream Theater instrumental to date (not counting live mash-ups such as Instrumedley).
Some lyrics of As I Am were inspired by Dream Theater's 2003 summer tour with Queensryche, described by Mike Portnoy as an "irksome series of shows." According to Portnoy, Queensryche guitarist Mike Stone tried giving John Petrucci tips on playing guitar, leading Petrucci to write the lyrics. Jordan Rudess played the final note in the album (In The Name of God minute 14:8) with his nose as shown in Making The Train of Thought documentary, Mike Portnoy approved the take in the video while he was filming.
"As I Am" – 7:47 (Petrucci)
"This Dying Soul" – 11:28 (Portnoy)
"Endless Sacrifice" – 11:23 (Petrucci)
"Honor Thy Father" – 10:14 (Portnoy)
"Vacant" – 2:58 (LaBrie)
"Stream of Consciousness" – 11:16 (instrumental)
"In The Name of God" – 14:16 (Petrucci)