Armed with a recording contract with September Gurls, in 1996 the band added analog synthesizer player Flip Osman and saxophonist/guitarist/singer Charlie Horshack, swelling their ranks and expanding their sonic palette, and this lineup released Killing You With Rock in 1998.
The following year, they were featured on a split 7-inch vinyl single with Italian band Kryptasthesie, contributing a very rare live version of their song "Jason Bill", a tribute to the erstwhile Charalambides guitarist.
The year 2000 was an active year for the Linus Pauling Quartet: they were invited to Seattle, Washington, to play at the fourth Terrastock psychedelic music festival alongside such musical luminaries as Bardo Pond, Moe Tucker, and Ghost; and they released Ashes in the Bong of God, a "concept album" related to their ongoing saga of the "bongs of power", alien "bug people," and "the Great Singularity," issued on double vinyl in Europe through the September Gurls label and on CD in the United States through the Fleece label.
All Things Are Light, self-released in conjunction with Camera Obscura on purple vinyl and made up primarily of some of the band's heaviest music to date, garnered a considerable number of positive reviews upon its release in December 2007.
On the heels of this release, the band was again invited to perform at Terrastock in June 2008, this time in Louisville, Kentucky, resulting in one of their most memorable shows, playing alongside such notable psychedelic groups as MV & EE, Robert Schneider's Thee American Revolution, Damon & Naomi, and Kawabata Makoto.
In January 2013, the Linus Pauling Quartet released Assault on the Vault of the Ancient Bonglords, a three-disk anthology covering their earliest recordings from 1994 all the way through 2010, packaged with a fully playable Dungeons & Dragons-style dice-based roleplaying game module, and a purple 20-sided die.
In July 2017, the group contributed side one to the Vincebus Eruptum label's third Psychedelic Battles split LP with Colt38, including their final masterpiece, "Jolakottur," the lyrics of which were derived from Icelandic folklore.