Shortly after Yoshimi and The Soft Bulletin, the Flaming Lips released two EPs in the same vein of their previous album's robotic theme which contain remixed songs from Yoshimi, Fight Test and Ego Tripping at the Gates of Hell.
They also appeared on the track "Marching the Hate Machines (Into the Sun)" on the Thievery Corporation album The Cosmic Game.
In 2002 they were invited to work with The Chemical Brothers.
Steven Drozd performed lead vocals, while Wayne Coyne performed harmony vocals, on the  single "The Golden Path", which was included on The Chemical Brothers compilation album, Singles 93-03.

In 2002, they performed as the opening act, as well as the backup band, for singer Beck on his Sea Change tour.
In the summer of 2004, it was announced that the Flaming Lips would appear among the headliners on the 2004 Lollapalooza tour, alongside such artists as Sonic Youth and Morrissey; however, the tour was canceled because of lack of revenue.
Also in 2004, the band recorded the song "SpongeBob and Patrick Confront the Psychic Wall of Energy" for the soundtrack of The SpongeBob SquarePants Movie.
Following the concerts' cancellation, the band entered Tarbox Road Studio with producer Dave Fridmann and began work on their eleventh album, the more organic-sounding At War with the Mystics.
The record, aimed to be a more guitar-based and heavier effort than recent albums, featured more politically conscious lyrics than any of their previous releases, and was released in April 2006 to a mixed yet mostly positive reception.

In 2005 the band was the subject of a documentary called Fearless Freaks, featuring appearances by other artists and celebrities such as Gibby Haynes, The White Stripes, Beck, Christina Ricci, Liz Phair, Juliette Lewis, Steve Burns, Starlight Mints, and Adam Goldberg.
In that same year, the Flaming Lips contributed a version of "Bohemian Rhapsody" to the album Killer Queen: A Tribute to Queen.
Also in this year, the Flaming Lips released the DVD VOID (Video Overview in Deceleration), which chronicles all of their ventures into music video that have been produced since they signed with Warner Bros in 1991.
In October 2005, the Flaming Lips recorded a cover of "If I Only Had a Brain" for the soundtrack of the video game Stubbs the Zombie, which features modern rock bands covering songs from the 1950s and 1960s.
Additionally, the band released one new song, "Mr. Ambulance Driver", for the soundtrack of the 2005 film Wedding Crashers (a slightly edited version of the song found its way onto the new record).

The band released two singles from At War With the Mystics: "The W.A.N.D.", which was featured in a Dell commercial and which was originally put out as a download-only single in early 2006, and "The Yeah Yeah Yeah Song", which became their highest-charting single on the UK Singles Chart, peaking at No.
 16.
A 4-track EP, entitled It Overtakes Me, was released later in the UK that year.
The only instrumental on the album, "The Wizard Turns On... The Giant Silver Flashlight and Puts on His Werewolf Moccasins", earned a 2006 Grammy Award for Best Rock Instrumental Performance, making it twice in a row the Lips have been nominated in that category and won.

Following the April 4, 2006 release of At War with the Mystics, the band began a tour to support the album in the United Kingdom, including a finale at the Royal Albert Hall and performances at the O2 Wireless Festival.
At the Leeds England date of the festival, the band opened for The Who, of whom they are long standing fans.

The band continued to tour throughout the fall of 2006 stopping in Montreal, the Virgin Festival on the Toronto Islands, Atlantic City's House of Blues, The University of Vermont in Burlington, their hometown Oklahoma City, the Austin City Limits Music Festival in Austin, Texas, and New York City, NY as well as several other cities.
The homecoming show in Oklahoma City was performed at the Zoo Amphitheater and included the unveiling of a new UFO stage prop, and would provide footage for the U.F.O.s at the Zoo concert DVD.

On December 5,
Shortly after Yoshimi and The Soft Bulletin, the Flaming Lips released two EPs in the same vein of their previous album's robotic theme which contain remixed songs from Yoshimi, Fight Test and Ego Tripping at the Gates of Hell. They also appeared on the track "Marching the Hate Machines (Into the Sun)" on the Thievery Corporation album The Cosmic Game. In 2002 they were invited to work with The Chemical Brothers. Steven Drozd performed lead vocals, while Wayne Coyne performed harmony vocals, on the  single "The Golden Path", which was included on The Chemical Brothers compilation album, Singles 93-03.
In 2002, they performed as the opening act, as well as the backup band, for singer Beck on his Sea Change tour. In the summer of 2004, it was announced that the Flaming Lips would appear among the headliners on the 2004 Lollapalooza tour, alongside such artists as Sonic Youth and Morrissey; however, the tour was canceled because of lack of revenue. Also in 2004, the band recorded the song "SpongeBob and Patrick Confront the Psychic Wall of Energy" for the soundtrack of The SpongeBob SquarePants Movie. Following the concerts' cancellation, the band entered Tarbox Road Studio with producer Dave Fridmann and began work on their eleventh album, the more organic-sounding At War with the Mystics. The record, aimed to be a more guitar-based and heavier effort than recent albums, featured more politically conscious lyrics than any of their previous releases, and was released in April 2006 to a mixed yet mostly positive reception.
In 2005 the band was the subject of a documentary called Fearless Freaks, featuring appearances by other artists and celebrities such as Gibby Haynes, The White Stripes, Beck, Christina Ricci, Liz Phair, Juliette Lewis, Steve Burns, Starlight Mints, and Adam Goldberg. In that same year, the Flaming Lips contributed a version of "Bohemian Rhapsody" to the album Killer Queen: A Tribute to Queen. Also in this year, the Flaming Lips released the DVD VOID (Video Overview in Deceleration), which chronicles all of their ventures into music video that have been produced since they signed with Warner Bros in 1991. In October 2005, the Flaming Lips recorded a cover of "If I Only Had a Brain" for the soundtrack of the video game Stubbs the Zombie, which features modern rock bands covering songs from the 1950s and 1960s. Additionally, the band released one new song, "Mr. Ambulance Driver", for the soundtrack of the 2005 film Wedding Crashers (a slightly edited version of the song found its way onto the new record).
The band released two singles from At War With the Mystics: "The W.A.N.D.", which was featured in a Dell commercial and which was originally put out as a download-only single in early 2006, and "The Yeah Yeah Yeah Song", which became their highest-charting single on the UK Singles Chart, peaking at No. 16. A 4-track EP, entitled It Overtakes Me, was released later in the UK that year. The only instrumental on the album, "The Wizard Turns On... The Giant Silver Flashlight and Puts on His Werewolf Moccasins", earned a 2006 Grammy Award for Best Rock Instrumental Performance, making it twice in a row the Lips have been nominated in that category and won.
Following the April 4, 2006 release of At War with the Mystics, the band began a tour to support the album in the United Kingdom, including a finale at the Royal Albert Hall and performances at the O2 Wireless Festival. At the Leeds England date of the festival, the band opened for The Who, of whom they are long standing fans.
The band continued to tour throughout the fall of 2006 stopping in Montreal, the Virgin Festival on the Toronto Islands, Atlantic City's House of Blues, The University of Vermont in Burlington, their hometown Oklahoma City, the Austin City Limits Music Festival in Austin, Texas, and New York City, NY as well as several other cities. The homecoming show in Oklahoma City was performed at the Zoo Amphitheater and included the unveiling of a new UFO stage prop, and would provide footage for the U.F.O.s at the Zoo concert DVD.
On December 5, 
The Flaming Lips