After touring for Burn My Eyes, Machine Head entered the studio to record its second studio album, The More Things Change..., with Richardson producing and mixing for a second time. The album was released on March 25, 1997, and debuted at number 138 on the Billboard 200 albums chart. Machine Head toured on the first Ozzfest for the first tour in support of the album. Mader showed up to a practice session late, high on methamphetamine, cursing at and insulting the band members; and quit the band later that day. Ahrue Luster replaced him and finished touring, while Mader toured with Soulfly in support of their self-titled debut album.
After three years of touring and working with producer Ross Robinson, Machine Head released its third studio album, The Burning Red, on August 10, 1999. The band added new elements to its music, including rapping vocals, a move which some believe to have been influenced by Ahrue Luster himself. This album and the band's change in image/musical direction (nu metal/alternative metal) was highly criticized, with critics and fans alike accusing the band of "selling out". Nevertheless, McClain stated they weren't trying to sound like popular bands but "wanted to sound different". Rick Anderson of Allmusic stated Machine Head was "sounding a bit looser and less constricted musically than they have in the past". The Burning Red became Machine Head's top selling album for a number of years, and debuted at number 88 on the Billboard 200.The album won the hearts of many new fans with such hits as "The Blood, The Sweat, The Tears" and "From This Day".Machine Head finished touring for The Burning Red, and entered a studio with producer Johnny K to record Supercharger. Debuting at number 115 on the Billboard 200, the album was released on October 2, 2001. The album met the same criticism as The Burning Red, especially for the ever-present rapping vocals. Blabbermouth.net reviewer Borivoj Krgin stated Supercharger "is likely to disappoint everyone who is expecting the Bay Area quartet to return to the ultra-testosterone-charged sounds of their first two albums".
Machine Head released a single for "Crashing Around You" as well as a music video. The video was released several weeks after the September 11, 2001 attacks, and was banned from MTV for the depictions of falling buildings. Roadrunner Records, expecting to make a fair profit from album promotions, dropped the band's funding, causing Machine Head to leave the label. At the same time the band was leaving Roadrunner, Luster departed from the band for musical differences.
By 2002, Machine Head has sold over 1.3 million albums worldwide, and overall Supercharger(mixed by Colin Richardson) would go on to sell an impressive 250,000 copies worldwide, but it would be their lowest selling album to date. Once the tour for the album had been completed, Machine Head and Roadrunner Records mutually decided to sever ties with regards to distribution in North America and around the world, however to fill the ties, the band released "Hellalive" (also mixed by Colin Richardson) which was a recording of a Brixton Academy, London set. In 2002 Ahrue Luster left the band and was temporarily replaced by Phil Demmel, who played in thrash band Vio-lence alongside Flynn. Demmel played some festival shows with Machine Head (including a headlining slot at the With Full Force festival in Germany). Then with Phil not being able to commit to the band, he and Machine Head parted ways. The remainder of the band starting writing songs for the next album (eventually Through the Ashes...), and hoping to get signed to a record label. They recorded a short demo, including a radio-style song called "Pins and Needles", and an Electronic Press Kit for the companies, also hoping they can get signed on the strength of their previous efforts. Nearly every record label in the music industry rejected the four track demo.
After Machine Head's European tour, Ahrue Luster returned to his family business and the band started writing together as a three-piece, while leaving a position open for Demmel. In March 2003, Demmel joined Machine Head as a full-time guitarist and started writing with the band. By June 2003, Machine Head entered a studio with Flynn producing. On October 27, 2003, Machine Head released Through the Ashes of Empires in Europe.
The band was turned down by multiple record labels in the United States, until Roadrunner USA, interested in the new album, offered Machine Head another record contract. Machine Head accepted the offer on the grounds that the band owns 100% of the music. On April 20, 2004, Through the Ashes of Empires was released in the United States with a bonus track for the Americans' long wait for the album's release. The album debuted at number 88 on the Billboard 200. The band released a single for "Imperium", the video for which received heavy rotation on MTV. Eduardo Rivadavia of Allmusic stated Through the Ashes of Empires "marked a return to form in no uncertain terms".
Machine Head headlined the True Metal stage at the 2005 Wacken Open Air festival to 40,000 fans—the band's largest headlining crowd. The band released a DVD containing a full sold out concert held at the Brixton Academy in December 2004, a documentary, and music videos. The DVD debuted at number 13 on the United States music video charts.
They also played in Dubai for the annual Dubai Desert Rock Festival in 2005. This was their first show in the Middle East.
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