The album was recorded from September 2006 to February 2007 at Avatar Studios in New York City, after the band's first break from summer touring in ten years.

The lyrics of the album were written by John Petrucci, James LaBrie, and Mike Portnoy about fictional, political, and personal topics, respectively.

[4] Dream Theater promoted the album on their Chaos in Motion world tour, which lasted a year and spanned 35 countries.

After recording their twentieth anniversary concert, Score, on April 1, 2006, Dream Theater rested for its first summer in ten years.

[11] Though Portnoy had some preconceived ideas for Systematic Chaos, he decided not to tell the rest of the band; leaving them to start with a "completely open palate".

[17] 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.

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.

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.

[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.

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.

Petrucci wrote the lyrics to "The Dark Eternal Night" about a pharaoh who has returned after dormancy as a monster to haunt a town.

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.

[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.

[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.

Over their seven album relationship with Warner Music Group, Dream Theater became disappointed at the lack of coverage they gave the band.

[4] Reviewing for Metal Invader, Nikos Patelis called the album, "energetic, sharp – edged, full of beautiful melodies and heavy riffs, long epic compositions".

[67] He called Dream Theater's instrumentalists "four masters of music that use their instruments as if they were their limbs", in addition to stating, "James LaBrie sounds more mature than ever".

[59] Reviewer Chad Bowar of About.com, wrote that "In the Presence of Enemies - Part I" is "an effective way to set the tone for the rest of the songs".

[70] In 2014, readers of Rhythm magazine voted Systematic Chaos the second greatest drumming album in the history of progressive rock.