In late 1998, IME returned to Toronto and reunited with Paul Northfield, who again shared production duties with Jag Tanna on the new sessions. These sessions were chronicled on the internet by Bruce Gordon, long considered the most fan-friendly member of the band (Gordon was known to answer fan emails dating back to the
Scenery and Fish years). Armando Borg returned in the place of Conte on percussion, though Mansilla remained IME's main percussionist. Rush frontman Geddy Lee was also brought in to provide bass for the album track "Good for Sule". While the Tannas were still the main contributors, they described the creative process as more open than before. The result was
Blue Green Orange, released in mid-1999. It was somewhat of a departure from earlier work, opting for more textured, spacier sounds and less of an emphasis on the band's hard-rock reputation. Still, the lead single, "Summertime in the Void", was a major rock hit in Canada and showed that the band was still commercially viable with a different singer and a change in sound. Subsequent singles "All Awake" and "When Did You Get Back from Mars?" also received solid radio and video airplay, but it was apparent that the band's commercial prime was over. The album's Gold status was seen as a disappointment by many compared to the previous albums. Tanna and Northfield won a Juno in 2000 for Best Recording Engineer, and the album was nominated for Best Album Design, but it received no musical nods.
IME came off the road and in 2001 the band members settled into their own Toronto studio, The Mother's Hip. However, this period was plagued with problems. Brian Byrne had ruptured his vocal cords and required surgery. Christian Tanna broke his forearm and was unable to play drums. After those injuries healed the band decided to scrap the entire session, which was reportedly filled with radio-friendly material, and start from the beginning. This occurred after a false story circulated in the media that the album was finished and tentatively titled
Save the Last Disco. Furthermore, the band also dealt with the EMI release of
Earth, Sky, and Everything in Between, an album of B-Sides and live recordings from the EMI years. The Tannas and Gordon issued a statement insisting the record was unauthorized and was nothing more than a cash grab by EMI. Edwin offered no comment on the album.
IME then went to work on the proper new album in 2002 with producer David Bottrill (alongside Jag Tanna), taking only a short break to headline the Canadian MTV Campus Invasion Tour, then releasing a song as a preview of the new material. The song "Juicy" was pressed as a promo single for the Vin Diesel movie
xXx, and despite no push from the label and no video, it received rock radio airplay on its own. It was later included on
The Quicksilver Meat Dream, released in early 2003. The album was an even larger departure from past works, with industrial elements replacing the Latin percussion (but not Mansilla, who still toured with the band), and a heavier, more progressive sound than ever before. However, Universal was unimpressed with the nearly-finished product and demanded radio-friendly singles, so the band returned to the studio to appease the label. Lead single "Like the Sun" was another Canadian rock hit, but despite its popularity, it failed to sell the record. Due to the dismal sales and arguments with the Tannas over the direction of IME, Universal withdrew all support from the band, leaving it to fund small tours and second single "No Coma" on its own. The song failed to be officially added to rock radio, the video received very limited play, and with that the band decided to end the album's run after only seven months. The band provided the theme songs for the MuchMusic TV shows
Much on Demand and
MuchLOUD, but otherwise went unheard in the media for the rest of the year. Universal officially dropped IME at the end of 2003.
In November 2003, I Mother Earth performed a special show in Barrie, Ontario, entitled "Live off the Floor". Largely considered by those present as their greatest live performance, the intimate, nearly four-hour show featured the band performing in the round of the Georgian College venue, with the crowd on all sides. IME played most of its back catalogue at the show, and it was thought to be the band's final performance.
Following the band's hiatus, Brian Byrne started a solo career, releasing two albums and one EP. Bruce Gordon joined the Blue Man Group lineup and pursued numerous side projects. Jagori Tanna founded a new studio and record label, UpperLeftSide music, as well as the production company Segment X Productions. Christian Tanna organized local Toronto rock and jazz events, and was in management roles with both UpperLeftSide music and The Venue, a concert-oriented nightclub in Peterborough.
In January of 2012 the band got together after a 9 year hiatus. A new song was offered up for download titles "We Got The Love" and numerous shows were planned, then more shows were added and even more into 2013.
In 1999, Clarknova released their first LP entitled Host. It was produced by Paul Northfield & Brad Nelson, and recorded at Great Big Music in Toronto, Studio Morin Heights in Quebec, as well as Newmarket Multimedia. The album included a re-make of their previous single "Stain" retitled "Re-Stain," this track had additional production by Mike Kerwin and was the only Tribal Stomp track that remained in Clarknova's setlist. The album was well received in the Toronto area, due to extensive self-promotion at concerts by the band. This in turn, caused 102.1 The Edge in Toronto to be overwhelmed with requests from fans to play the single "Johnny Under," causing the song to be inserted into high rotation. The band toured regularly throughout this time acquiring a growing fanbase. 
In 2002, the band recorded their follow-up album Annexia with Jagori Tanna from I Mother Earth as producer. Plans were set to release the disc, when guitarist Scott Wilson left the band due to personal reasons. Later, while touring the record, the band lost their second guitarist, Greg Caines, to similar circumstances. Scott was soon replaced by Dan Preston, who had performed engineering duties on both Clarknova records, and played guitar on the track "Exile At Home," and Greg was replaced by Pat Davies. The first single "Drown," followed by "Please Them," the video for which was played regularly on MuchLOUD. The band also released a third single entitled "Start Again (Velocity)." After a nationwide tour with I Mother Earth and Scratching Post, the band eventually broke up. The original line up of Kulba, Wilson, Caines, Ferguson and Lord reunited after seven years to perform one show only in Newmarket on December 18, 2010 as a part of York Aid at Glenway Country Club. A guest appearance from Dan Preston, who was in version 2.0, joined the band for the last song of the night "Johnny Under".
