Systematic Chaos

The first piece recorded, the twenty-five-minute epic "In the Presence of Enemies," was described by Petrucci as the "epitome of a Dream Theater creation".[18] He went on to describe the composition as "very progressive, very long"; also noting that it set a good tone for writing and recording the rest of the album.[18] Their longest recording since "Six Degrees of Inner Turbulence", it was split into two parts, due to it having a good open and close for the album at the same time. According to Portnoy, the band felt it was too long to open the album, but did not want to close the album with a long song, as they had with the twenty-four-minute title track of their last album Octavarium (2005).[19] The songs are normally played together in their entirety in live shows. During recording, the work was titled, "The Pumpkin King,"[20] and in the album's booklet, the song is given a subtitle, "The Heretic and the Dark Master."

The story of "In the Presence of Enemies" was inspired by a Korean manhwa named Priest, as Petrucci explains that not being a manga fan, precisely, "[...] I like it though. This one, I just stumbled upon and I really liked the content. It inspired me to take a different approach lyrically. You have to keep things interesting for yourself when writing new material so I just took this and ran with it. [...] Those types of lyrics are fun to write, you know? The dark subject matter, the dark master stuff. It's another way of writing, a fresh one to me."[21] He also summarizes the lyrics: "It's a story about somebody who loses himself and end struggles with the darkness, symbolized by the Dark Master. And the story ends up really being the darkness within and goes through the different phases where he has to fight demons and things like that.[22]

Petrucci said "Forsaken" is a story told through a "short song structure".[23] The song tells of a person who is visited at night by a vampiress. While the man thinks he is being taken away and being shown "wonderful things", he doesn't realize that the whole time he is getting his blood sucked, and is eventually taken, in the end, by the vampiress.[24] An animated music video of "Forsaken", produced by Gonzo and directed by Yasufumi Soejima, was released on January 26, 2008.[25][26] The band allowed Soejima artistic freedom with the design of the video,[27] which was set in a science fiction future instead of the present day.[25] During the production of the album, the working title for this song was "Jet Lag", and it was the sixth song to be written.[28]

"Constant Motion" was released as the first single from the album on April 27, 2007. It was first made available as a free download the same day by Roadrunner Records; it could be found at Roadrunner Records' Dream Theater sub-website for a limited time.[29] This song was also made available to download for the music video game Rock Band.[30] The song is considered as one of the hardest songs available for the game on both Guitar and Drums. Its working title was "Korma Chameleon", and was the second piece written.[31]

Mike Portnoy said that since it was one of the more aggressive, more driving songs on the album, that the lyrics were very much a metaphor for his Obsessive Compulsive Disorder. With everything he does for Dream Theater as well as his life in general, that his "wheels are always in constant motion", and that he's always juggling many different projects or responsibilities for the band at the same time. So the lyrics are a representation for whats going on in his head on any given day.[32]

The song was also accompanied by a music video, the first the band had produced in over a decade.[33] The video clip premiered on July 13, 2007 and was released as a free download, in two different formats, also for a limited time.[34] The band had not produced a music video since "Hollow Years" from Falling into Infinity (1997), citing lack of interest and lack of rotation on music channels for the latter. The video received considerable airplay on MTV2's Headbangers Ball and was voted as the second best music video of 2007 by the same;[35] it is arguably Dream Theater's most popular video since "Pull Me Under" in 1992.

Petrucci wrote the lyrics to "The Dark Eternal Night" about a pharaoh who has returned after dormancy as a monster to haunt a town.[36] The lyrics are heavily influenced by the short story Nyarlathotep by American horror fiction writer H.P. Lovecraft, even borrowing a lot of specific phrases from this story. The song contains an improvised continuum solo, performed by Rudess while the drum tracks were being recorded; the band members liked the solo enough to keep in the final recording.[37] In the October 2010 issue of Total Guitar Magazine, its readers voted the main riff of "The Dark Eternal Night" as the fourth greatest riff of the decade. During the making of the song, the title was, "N.A.D.S." ("North American Dream Squad") and it was the fifth song to be written.[38]

The sprawling, progressive midsection was not featured in the song's original edit, but is based around a riff that Rudess came up with in the control room, when listening to the original, more conservative instrumental section. "I was debating whether or not I should even bring it up, but then I got brave and said 'You know, I've got this weird idea.'"[39]

The Dark Eternal Night was the second of two songs released to the general public in advance of the album's release, with an in-studio video being released to YouTube in May 2007.

Portnoy wrote "Repentance" as the fourth part of his Twelve-step Suite,[40] a collection of songs from various Dream Theater albums which revolve around his journey through Alcoholics Anonymous. The song discusses steps eight and nine of the process, which deal with making a list of people whom one has wronged and, if possible, making direct amends with them.[41] Portnoy, who as of 2007 had been sober for 7½ years,[42] invited friends and fellow musicians Mikael Åkerfeldt, Jon Anderson, David Ellefson, Daniel Gildenlöw, Steve Hogarth, Chris Jericho, Neal Morse, Joe Satriani, Corey Taylor, Steve Vai, and Steven Wilson to record spoken apologies, regrets, and sorrows of their own,[43] which were featured throughout the song.[44] Portnoy dedicated "Repentance", "to Bill W. and all of his friends". During recording, the title of the track was, "Fisheye" and it was the seventh and final song to be written.[45] This saga is concluded in the band's tenth studio album Black Clouds & Silver Linings with "The Shattered Fortress".

"Prophets of War" was written by James LaBrie, who based the lyrics loosely on Joseph C. Wilson's book The Politics of Truth.[46] The lyrics talk about possible ulterior motives behind the Iraq War, while remaining "middle of the road".[46] The title is a play on words, where the "prophets" of the war, could also be gaining a "profit" from the War.[46] During the recording of the song, Portnoy suggested fans could voice certain lyrical chants.[47][48] In response to a message posted on the band's website[49] four hundred fans gathered outside the recording studio to record the chanting,[48] however only sixty could fit into the studio. The title of the track during recording was, "Carpet Babies" and it was the third song to be written.[50]

At 14:57, "The Ministry of Lost Souls" is the album's second longest track. Throughout the song's lyrics, Petrucci tells of a person who dies in the process of saving a woman from drowning. However, the woman who is saved is filled with "regret and sorrow" until she is able to re-unite with her rescuer. The title for the track during recording was, "Schindler's Lisp" and it was the fourth song to be written.[51]

• Complete album in 5.1 surround sound
• Chaos in Progress: the making of Systematic Chaos