Armed with yet another new member, Dream Theater entered BearTracks Studio once again to write and record their next album. Perhaps as a response to the backlash over Falling Into Infinity, this time their record label gave the band complete freedom with their music. The follow-up to "Metropolis Part 1" of Images and Words, which was written during the Falling Into Infinity sessions (but not used on that album), was taken off the shelf as the first composition for them to work on.

They decided to rewrite and expand the 20-minute song with a fresh, new band member into a complete concept album, with the story revolving around themes such as reincarnation, murder and betrayal. To avoid stirring up the fan base, a tight veil of secrecy enveloped the writing and recording process. The only things fans knew before its release were a track list that had been leaked against the band's wishes, and a release date. They knew nothing of the title, the music, or even the fact that it would be a concept album. In 1999, Metropolis Pt. 2: Scenes from a Memory was released to high critical acclaim. It was hailed as Dream Theater's masterpiece by many fans,and critics alike, despite only reaching #73 on the charts.[1] Scenes From A Memory is often compared to Queensrÿche's Operation: Mindcrime, another seminal progressive metal concept album released a decade earlier.[6]
A world tour that followed led the band into more countries than they had ever toured before, taking over a year to complete. For one extra special show, at the Roseland Ballroom in New York City, actor Kent Broadhurst was hired to play the role of the hypnotherapist, and gospel choir led by Theresa Thomason, (also present on the MP2 album as guest singers) was enlisted to play in certain sections of the show. This show, the last North American date of the tour, was recorded for the band's first DVD release. After many technical delays, Dream Theater fans finally got their hands on the DVD, entitled Metropolis 2000, in early 2001. Shortly after its release, the band announced that an audio version of the concert, with the entire four-hour long set list (much of which had to be cut from the DVD to save space), would be released shortly thereafter.
The covers of Live at the Marquee and Live Scenes From New York. Notice the silhouette of the World Trade Center within the flames on the right
The covers of Live at the Marquee and Live Scenes From New York. Notice the silhouette of the World Trade Center within the flames on the right
The cover for the CD version of the concert, titled Live Scenes From New York, showed one of Dream Theater's early logos (the Images And Words-era burning heart, modeled on the Sacred Heart) modified to show an apple instead of the heart, as an allusion to the Big Apple nickname given to New York City. In the flames above the apple was shown the New York City skyline, including the twin towers of the World Trade Center. In an unfortunate coincidence, the album was released on September 11, 2001 - the same day as the terrorist attack on the World Trade Center. The album was immediately recalled, but many copies were snapped up by Dream Theater collectors as a very rare piece of Dream Theater's history. It was re-released with revised artwork a short time later.

Dream Theater once again entered BearTracks Studios to record their sixth studio album. Four years after they first petitioned EastWest to allow them to release a double album, they finally got their chance with Six Degrees of Inner Turbulence. The first disc consisted of five tracks of 6-14 minutes in length, and the second disc was devoted entirely to the 42-minute title track, split into 8 parts, which is to date the longest song Dream Theater have written.
Six Degrees of Inner Turbulence ended up being received very well by critics and the press.[7] It was the most publicized of Dream Theater's albums since Awake, debuting on the Billboard charts at #46[1] and the Billboard Internet charts at #1.[8]
Throughout the next year and a half they toured the world once more, with an expanded live show including a select few special "album cover" gigs (see Cover songs section, below), in which they played Metallica's Master of Puppets and Iron Maiden's The Number of the Beast in their entirety.
At the completion of their promotional tour and various side projects, Dream Theater entered the studio to record what would become Train of Thought, their heaviest album to that point,[9] written in a mere three weeks.[10] The album was a critical success but it had a polarizing effect, alienating a fair portion of Dream Theater's fans who enjoyed the traditional progressive rock influence from bands such as Yes or King Crimson more than Dream Theater's modern muses like Tool and Metallica[citation needed]. Regardless, it expanded the band's fan base into new territory, that of mainstream heavy metal and alternative metal[citation needed].
Their next move was to release another live CD/DVD combination, this time recorded at the famous Nippon Budokan Hall in Tokyo, Japan on their Train of Thought world tour. Live at Budokan was released on October 5, 2004, and further propelled Dream Theater's reputation as one of the premier live acts in progressive metal[citation needed].
Upon the completion of their Train of Thought promotional tour in 2004, Dream Theater entered the Hit Factory studios in New York City to record their eighth album. As it turned out, they would be the last group ever to record in that famous studio, and after they wrapped up their final session, the lights were turned off at the studio forever.
The latest album, Octavarium, was released on June 7, 2005 and took the band's sound in yet another new direction. Among its eight songs is a continuation of Portnoy's "Alcoholics Anonymous" suite ("The Root of All Evil", steps 6-7 in the 12-step plan), as well as the title track itself, an epic rivaling A Change of Seasons and which spans several musical styles in its 24-minute running time[citation needed]. Like nearly every album by the band, Octavarium has received mixed reviews from fans and been the subject of spirited debate. In particular, some fans thought that the band wore its musical influences too prominently on their sleeves (e.g. "Never Enough" has been compared to Muse's Stockholm Syndrome[11] and the relatively radio-friendly "I Walk Beside You," which combines a sound reminiscent of U2 and Coldplay.[12] Octavarium was the last album under their seven-album deal with Elektra Records, and the band subsequently left the label.
Dream Theater toured extensively throughout 2005 and 2006 to celebrate their 20th Anniversary as a band, including a headlining spot on Gigantour. During a show on August 2, 2005 in Dallas, the band paid tribute to Pantera's late guitar virtuoso Dimebag Darrell by performing Cemetery Gates as an encore; what made the performance even more remarkable was the unexpected appearance of fellow musicians Russell Allen, Burton C. Bell and Dave Mustaine, who joined the band on stage to perform parts of the song.[13]
Dream Theater later departed from Gigantour and continued their own series of concerts; including a show at the famous Radio City Music Hall in New York City on April 1st, 2006 with "the Octavarium Orchestra". The show was recorded for a CD/DVD called Score, released on August 29, 2006 through Rhino Records.
On February 8, 2007, it was announced that Dream Theater has signed with Roadrunner Records and will be releasing their ninth studio album in June 2007, titled Systematic Chaos