There, he performed with a variety of artists both in and out of the jazz community, among them John Zorn, Eugene Chadbourne, Elliott Sharp, Wayne Horvitz, Butch Morris, and the dB's. He is a founding member of the Microscopic Septet and, after its demise, went on to lead Phillip Johnston's Big Trouble and Phillip Johnston's Transparent Quartet.

In addition to commissioned works in conjunction with a number of theatrical and dance productions, Johnston earned notoriety for his eclectic film work, scoring pictures by directors including Doris Dorrie, Philip Haas, and Paul Mazursky. Following the 1992 breakup of his group the Microscopic Septet, he soon resurfaced fronting the band Big Trouble, debuting with a self-titled LP on the Black Saint label. After scoring the film noir The Unknown, Johnston and Big Trouble returned in 1996 with Flood at the Ant Farm; Normalology followed a year later.

In 1998, Johnston enjoyed a release on Zorn's Tzadik label, Music for Films, and a release on Koch with his newly formed Transparent Quartet, The Needless Kiss. The group finds Johnston with tuba player and bassist Dave Hofstra, pianist/baritone saxophonist Joe Ruddick, and vibraphonist Mark Josefberg. The band followed up their debut with The Merry Frolics of Satan: The Georges Meiles Project in 1999. ~ Jason Ankeny