The band released two live recordings in 2001, Live Frogs Set 1 and Live Frogs Set 2. Set 1 is a mix of covers and originals, including "Thela Hun Ginjeet" (King Crimson) and "Shine On You Crazy Diamond" (Pink Floyd). Set 2 is a live cover of the entire Pink Floyd album, Animals. A studio album was also released in 2002 entitled Purple Onion.
In August 2000, Claypool created a new line-up of the Frog Brigade and took it on a tour that fall. The band consisted of Jay Lane on drums and Todd Huth on guitar, who had worked with Claypool in Sausage (which in itself was a re-formation of the first line up of Primus), guitarist Eenor, who got a place in the band by winning a mail-order competition, Jeff Chimenti, the keyboardist from Ratdog (Jay Lane also has worked with Ratdog), and Skerik continuing on saxophone. This version of the band played a show consisting of two sets - the first filled with covers and songs from Claypool's previous bands, and a second set where the band would play all of the Pink Floyd album, Animals.
After this tour, the Brigade released two live recordings, both taken from the Autumn 2000 concerts by the band in San Francisco. Live Frogs, Vol. 1 contained material from the first, free-form set, and Live Frogs, Vol. 2 was a recording of the band performing Animals.
In the summer of 2001 the band comprised of Claypool, Skerik, Eenor and a new drummer, Paul Svena. Les began writing new material and they began playing single-set live shows. In 2002, Mike Dillon was added as a percussionist and the Frog Brigade recorded their only studio album to date, Purple Onion.
In 2003, Eenor left the band and guitarist Brian Kehoe joined. Throughout their touring schedule the band has changed drummers multiple times. Drummer Paulo Baldi also entered the rotation in 2003. Baldi, formerly of the Bay Area trio Deadweight, who have disbanded, is a natural fit along the lines of Tim Alexander and Jay Lane.
In 2004 Claypool formed a new jamband, Colonel Claypool's Bucket of Bernie Brains, with guitarist Buckethead, keyboardist Bernie Worrell, and former Primus drummer Bryan Mantia (aka Brain). This band had much the same genesis as the Frog Brigade; Formed to play at the Bonnaroo Festival of that year, it has since gone on the road, and recordings have become subsequent live albums.
As of Spring 2007, the Frog Brigade has not recorded any new material since Purple Onion, and the band has not gone on a major tour since Summer 2003, but has occasionally re-formed to play other one-off shows and music festivals. Claypool toured 2006 and 2007 with Paulo Baldi, Gabby La La, Mike Dillon and Skerik as Les Claypool's Fancy Band.