In 1991, the label released his solo debut, Whiplash Boychild. The ambitious effort was unlike anything Connelly or Wax Trax! had issued before, recalling Bowie and Bolan at times and experimenting with avant-garde song structures here and there. Also that year he hooked up with another Chicago-based industrial label, Invisible, and became involved in their Pigface, Murder Inc., and Damage Manual projects, which meant he was now rubbing shoulders with Geordie Walker of Killing Joke and former Public Image Ltd. drummer Martin Atkins. Atkins would then become involved in 1992's Phenobarb Bambalam, Connelly's dark and introspective sophomore solo effort. Shipwreck from 1994 was much more uplifting and referenced the singer's early love of glam rock with sharp guitars and Bowie-esque vocals. As the Wax Trax! label began to implode, Connelly spent 1996 working with industrial giants KMFDM for their XTORT album and recorded an a cappella version of the Wire song "A Mutual Friend" for Whore: Tribute to Wire. With Wax Trax! out of the picture, 1997's The Ultimate Seaside Companion (Revisited) appeared on Invisible. The album was more acoustic, more folk, and featured multi-instrumentalists Chris Bruce and Jim O'Rourke as members of the loosely knit backing band the Bells. Bruce would return for a second effort with the Bells, Blonde Exodus, which landed in 2001 with a much more muscular sound. Also appearing in 2001 was Largo, an album with Bill Rieflin that the two first imagined in 1990.
In 2002, Connelly was back on his own with Private Education, an album released by the Invisible-related label Underground, Inc. That same year the label also released the two-CD Initials C.C., which collected "outtakes, rarities and personal favorites" from all the various projects Connelly had been involved with, save Ministry. He was back on Invisible proper for the 2004 release Night of Your Life, which received rave reviews across the board. In 2006 the six-CD set simply titled Box Set appeared on Invisible. The box collected all of Connelly's work for Invisible and Underground, Inc. along with the new live disc Lounge Ax, Bottle, and Elsewhere. Members of Joan of Arc, U.S. Maple, and Town and Country appeared on his improv-minded 2007 effort The Episodes. The album was released by Durtro Jnana -- home to eccentrics like Current 93, Nurse with Wound, and Antony and the Johnsons -- and was recorded partially outdoors. Connelly returned to somewhat more conventional song structures for 2009's Pentland Firth Howl, a collection of songs about his native Scotland, whose titles were all latitudinal and longitudinal geographic points. The gloriously lonely album was pretty much performed on acoustic guitar and harmonica. Connelly is among the most restless -- if soft-spoken -- musicians when it comes promoting his own work. In 2010 he released the wonderfully ambitious How This Ends on Lens Records. It is a two-part suite comprised of two long parts of the title track. Connelly produced it at a number of Chicago studios and enlisted a group of friends -- including James "Marlon" Magas, Tania Bowers, Zak Boerger, Sanford Parker, David Levine, Gordon Sharp, Izi Coonagh, and Brent Gutzeit -- in the recording process. The more straight-ahead rock album Artificial Madness followed in 2011.
In 2013, Connelly released the limited-edition Day of Knowledge, on klanggalerie. The recording looked back at some of the dissonant explorations of his Fini Tribe days, his art song work on The Episodes, and drones and electro-acoustic experimentation.
Decibels from the Heart appeared in 2015 from Cleopatra. The set featured another top-flight cast of musicians and on over half the tracks, placed the singer/songwriter in duets with female vocalists including Meshell Ndegeocello, Rebecca Pidgeon, My Brightest Diamond, and Claire Massey. ~ David Jeffries