After Ethyl Meatplow's breakup, Bozulich went in a very different direction, crafting mournful and eerie alt-country with the Geraldine Fibbers, who were named after Bozulich's imaginary childhood friend. 1995's Lost Somewhere Between the Earth and My Home introduced the group's searing-yet-delicate attack, which was expanded and amplified with 1997's Butch, largely due to the addition of experimental guitarist Nels Cline as a new Fibber. Despite wide acclaim for Butch's searching, ambitious music, the album ended up being the Fibbers' final statement (Sympathy for the Record Industry's What Part of Get Thee Gone Don't You Understand?, which was also released in 1997, was a collection of demos and EP tracks). The band's label, Virgin, wanted a solo album from Bozulich instead of another Geraldine Fibbers release, and the group folded under the pressure. However, Bozulich and Cline's collaboration continued in the form of Scarnella, whose self-titled 1998 album of experimental, improvisation-heavy pieces was even more abstract and adventurous than Butch and led to Bozulich devoting more of her time to improvised music. She also delved into scoring, writing music for the 2002 film By Hook or by Crook and for a production of the play The Maids by Jean Genet.

In 2003 she released her first solo album, an experimental but spiritually faithful reinvention of Willie Nelson's classic Red Headed Stranger that featured Cline, as well as Devin Hoff, Carla Kihlstedt, Marka Hughes, Jenny Scheinman, and Nelson himself among her collaborators. The album won Bozulich virtually unanimous acclaim that spilled over to the following year's mini-album I'm Gonna Stop Killing, which expanded on Red Headed Stranger's approach with improvisations based on the album and covers of Neil Young and Marianne Faithfull songs. For 2006's Evangelista, Bozulich moved to Constellation and worked with many of that label's brightest lights, including members of A Silver Mt. Zion and Godspeed You Black Emperor!, as well as Cline and Shahzad Ismaily, a multi-instrumentalist who also performed and recorded with Bozulich's more straightforward rock band, the Night Porter.