Originally intending to include Fates Warning guitarist Jim Matheos, Morse and Portnoy tapped The Flower Kings guitarist/vocalist Roine Stolt when Matheos was unable to participate. The band completed their lineup by adding bassist and progressive rock veteran Pete Trewavas from the group Marillion and Edison's Children.
The name of the group was originally planned to be "Second Nature," but was changed to Transatlantic at the suggestion of the cover artist Per Nordin.
Their first album, 2000's SMPT:e (a play on words, as both a combination of the members' last initials, as well as a common machine time protocol used in high end recording studios) received strong critical reviews, including "some of the best progressive rock music ever written" (Robert Taylor in Allmusic).
A subsequent tour of the United States led to a double live CD, Transatlantic Live in America, and a video of the same name. The band showed their musical heritage on the live CD, presenting covers of The Beatles' "Strawberry Fields Forever", as well as a medley of Genesis' epic "Watcher of the Skies" and "Firth of Fifth".
Though SMPT:e contained the 31-minute opus "All of the Above", the band's second studio album, 2001's Bridge Across Forever, found the band flexing their muscles further in the long form for which progressive rock is known. The CD contained just four tracks, the 26-minute "Duel With the Devil", the 14-minute "Suite Charlotte Pike", and the 26-minute "Stranger in Your Soul" making up the bulk of the disc, with the title track coming in at a relatively scant five minutes. The limited edition also contains a cover of Pink Floyd's "Shine on You Crazy Diamond". In November 2001 the band toured Europe. As an added bonus for progressive metal fans, Daniel Gildenlöw of the band Pain of Salvation sat in throughout the tour as a "fifth member" of the band, playing keyboards, guitars, percussion, and vocals.
Morse left his regular band Spock's Beard in October 2002, stating "God wants me to do something else," which meant leaving the mainstream prog scene to launch a new career as a Christian musician. This move also included ending his activities for Transatlantic. Portnoy reacted: "This spells the end of Transatlantic as I wouldn't possibly consider continuing it without him." A live DVD of the band's then-last tour was released in late 2003, featuring all aforementioned epics with "Suite Charlotte Pike" mixed with the Abbey Road medley by the Beatles.
In the years to follow Morse continued to collaborate with Portnoy both in the studio and on stage. Morse' concerts frequently included one or more Transatlantic songs. A three-quarter reunion took place on August 23, 2008, when Stolt and Portnoy joined Morse at the Three Rivers Prog Fest in Pittsburgh for "We All Need Some Light" and "Stranger In Your Soul."
On April 16, 2009, it was officially announced that the band had reunited and begun work on a third studio album. The album was released in October 2009 and consisted of a single 77-minute title-track The Whirlwind. A special edition of the album was also released, including a second disc with four additional original tracks and four cover tracks. Additionally, a deluxe edition was released, which included a DVD documenting the making of the album. The album reached No. 21 on the U.S. Billboard Heatseekers chart.
The band toured North America and Europe in April–May 2010 in support of The Whirlwind. Dubbed the Whirld Tour, the band was again joined by Daniel Gildenlöw on stage. End 2012 Morse compiled a CD called A Proggy Christmas performed by The Prog World Orchestra. The Prog World Orchestra has different well known progressive rock names as members on each track. One of the ten songs on this album is "Silent Night/We All Need Some Light" and on this instrumental track The Prog World Orchestra is composed of the four members of Transatlantic.
In February 2013, the new Neal Morse band (with Mike Portnoy) and The Flower Kings started a European tour together which was followed by a gig in Los Angeles in May. Each band performed a set with their own songs and the encore set featured Transatlantic songs performed by Morse, Portnoy and Stolt supported by members of the two bands with special guests Jonas Reingold and Randy George alternating on bass. The encore ends with eleven musicians on the stage.
On March 10, 2013, Pete Trewavas announced at the Marillion Weekend Convention in Port Zélande, the Netherlands, that he would be going to Nashville in the Summer to record new material with Transatlantic. Neal Morse confirmed this to DPRP.
On May 30, 2013, Mike Portnoy announced that they had finished writing a new Transatlantic album. It features five songs (two epics and three "normal length" ones) plus 8 covers for the bonus disc. The album was released in January 2014. A world tour of the United States and Europe followed, including a special performance on the "Progressive Nation at Sea" cruise created by Mike Portnoy. The band played two shows, with the first featuring the entire "Kaleidoscope" album and the second including guest performances by famous progressive rock artists such as Jon Anderson of Yes. On Sept 11, 2014, Kaleidoscope won 'Album of the Year' at the third annual Progressive Music Awards.