In 1986 Mori formed a duo with bassist and vocalist Luli Shioi, Tohban Djan, which eventually recorded Poison Petal (Nato, 1989).

The Worlds Of Love (Review, 1989) was a more experimental trio with Cinnie Cole and David Garland.

Her career in improvised music for drum-machines began with a collaboration with Japanese vocalist Tenko, Death Praxis (What Next, 1993) and a collaboration with Belgian avantgarde vocalist Catherine Janiaux, Vibraslaps (june 1992 - RecRec, 1993), both collections of "songs" that Mori filled with surreal percussive soundscapes. Catherine Janiaux had previously played in Aksak Maboul and worked with Tim Hodgkinson of Henry Cow fame and with Charles Hayward of This Heat fame. Her brief songs range from demented skits like Shiver to Renaissance madrigals like Missing, and from children's nursery rhymes like Ce Grand Neant to neoclassical lieder like Smell.

On the first album credited to her, Painted Desert (february 1994 - Avant, 1995), Ikue Mori was really just in charge of programming the electronic drumming. The real heroes of the album, which sounds like a glitchy remix of Ennio Morricone’s spaghetti-western soundtracks, are guitarists Robert Quine (mostly in the twangy, reverbed lead) and Marc Ribot (mostly the atmospheric undercurrent). They concoct the mesmerizing post-psychedelic guitar interplay of Mojave, the languid and ghostly Medicine Man, the hallucinated Santa Ana Excursion, and the galopping hard-rock Desperado, like a meeting of Duan Eddy and Eddie Van Halen. Mori creates a rhythm halfway between a samba and a country trotting for El Dorado, but the rest of the beats are quite trivial. The album ends with the slow, repetitive, nine-minute trance of Painted Desert over a tactful swinging beat with the guitars progressively emitting more and more desert sounds.

This first album was followed by Hex Kitchen (Tzadik, 1995), a sort of programmatic manifesto that employs distinguished improvisers in duos, trios and quartets, and especially by Garden (may 1996 - Tzadik, 1996), containing five long meditations for drum machines and samplers (The Pit And The Pendulum, Abacus - Blue Parrot, Tool Box - Loops, Bamboo Battle, Donkey Diversion - Gull - Moon Desert). These works established her as a quirky artist straddling the border between electronic soundpainting, the new wave, and free-jazz improvisation.

Death Ambient (june 1999 - Tzadik, 1995) was a prog-rock trio with bassist Kato Hideki and guitarist Fred Frith that also released Synaesthesia (Tzadik, 1999) and Drunken Forest (Tzadik, 2007).

Collaborations included: Bit-Part Actor (november 1994 - Braille, 1997), with vocalist Amanda Stewart, guitarist David Watson, reed player Jim Denley, and Rik Rue on tapes and sampler; Mystery (april 1998 - Tzadik, 1998), another work with Tenko, plus Anthony Coleman on organ, Eyvind Kang on violin and Erik Friedlander on cello; and, more importantly, Ile Bizarre (july 1997 - Ambiances Magnetiques, 1998), with Diane Labrosse on sampler and Martin Tetreault on turntables.

B/Side (august 1997 - Tzadik, 1998) collects music for the cinema.

One Hundred Aspects Of The Moon (Tzadik, 2000) is music for small chamber ensemble (Anthony Coleman, Eyvind Kang, Erik Friedlander, Hideki Kato) and vocals (Theo Brickmann).

Later (Victo, 2000), with Fred Frith and Mark Dresser, and SYR 5 (SYR, 2000), with Keith Gordon of Sonic Youth and DJ Olive, are minor collaborations.

Mori started a new career with Labyrinth (Tzadik, 2000), her first album of laptop music. Now a full-fledged laptop musician, Mori formed Mephista, a trio with pianist Sylvie Courvoisier and drummer Susie Ibarra, and released Black Narcissus (Tzadik, 2002).

Hemophiliac (Tzadik, 2002) is a collaboration with Mike Patton and John Zorn.

Acoustiphobia Vol 1 (Sublingual, 2001) is a live improvisation among Ikue Mori and Christian Marclay and Elliott Sharp.

Phantom Orchard (Mego, 2004) started a collaboration with Zeena Parkins (harp, keyboards). The impressionistic pieces evoke a more abstract Before And After Science (Brian Eno).

Myrninerest (Tzadik, 2005), a tribute to the paintings of Madge Gill, is another powerful creation at the laptop, and perhaps her most emotional and personal statement.

Alien huddle (december 2006) is a trio with saxophonist Lotte Anker and pianist Sylvie Courvoisier.

Class Insecta (december 2008) was a solo electronic album that introduced dance beats in her soundscapes.

Parkins, Ikue Mori, Cyro Baptista (percussion), Josh Wuillen (steel drums) and two vocalists recorded another Phantom Orchard album, Orra (july 2007). Parkins and Mori added the all-female quintet of Maja Solveig Kjelstrup Ratkje (voice and electronics), Hild Sofie Tafjord (French horn) and electronics), Sara Parkins (violin), Maggie Parkins (cello) and Shayna Dunkelman (percussion) on the Phantom Orchard's Trouble In Paradise (november 2008).

Near Nadir (august 2010) documents a live collaboration between percussionist Mark Nauseef, Ikue Mori (on electronics), Evan Parker (on soprano sax), and bassist and composer Bill Laswell.

The duo of Ikue Mori (electronics) and Steve Noble (drums and percussion) recorded Prediction And Warning (november 2011 - Fataka, 2013).

The live Scrumptious Sabotage (march 2012 - Bocian, 2013) features music composed and performed by Norwegian composer and vocalist Maja Solveig Kjelstrup Ratkje and by Ikue Mori.

Zeena Parkins' and Ikue Mori's Phantom Orchard returned with Through The Looking-Glass (october 2013), featuring Sara Parkins (violin), Maja Solveig Kjelstrup Ratkje (vocals and electronics), Maggie Parkins (cello) and Sylvie Courvoisier (piano).

In Light Of Shadows (Tzadik, 2015) is an all-electronic album, notably the 15-minute Koya Hijiri/ Holy Man Of Mount Koya.

Obelisk (september 2016) featured Sylvie Courvoisier on piano, Okkyung Lee on cello and Jim Black on drums, with a ten-minute version of Koya Hijiri/ Holy Man Of Mount Koya.

Highsmith (february 2017) featured Mori on electronics and Craig Taborn on piano, notably in the ten-minute Mermaids On The Golf Course.

IPY (november 2019) documents a live performance by the trio of Ikue Mori (electronic drum), Phew (voice and synthesizer) and Yoshimi Yokata (aka YoshimiO) on drums, voice and synthesizer.

Prickly Pear Cactus (february 2020) was the outcome of a remote Internet collaboration between Ikue Mori (electronics), Satoko Fujii (piano) and Natsuki Tamura (trumpet) during the covid pandemic.

A Mountain Doesn't Know It's Tall (january 2015) documents duets between Fred Frith (home-made instruments, various toys and objects, electric guitar) and Ikue Mori (laptop electronics).

Mori (on laptop), Brian Marsella (on keyboards) and Sae Hashimoto (percussions) recorded at their respective homes Archipelago X (Tzadik, 2021) during the covid pandemic of 2020.

The trio of Ikue Mori (electronics), Yuko Fujiyama (piano, voice) and Graham Haynes (cornet, electronics) recorded Quiet Passion (december 2019)

Tracing The Magic (february 2022) contains chamber pieces in which Mori, playing electronic instruments, teams up with a varying cast of improvisers. The Japanese shamanic-psychedelic invocation of Moving Off The Earth is sculpted with percussionist Sae Hashimoto (normally a baroque timpanist in symphony orchestras and a member of the avantgarde quartet Yarn/Wire) and veteran 66-year-old rock vocalist Makigami Koichi (member of Hikashu since 1978, also active in theater and ballet, and a John Zorn associate). The eleven-minute abstract labyrinth of You Better Grow Up (perhaps a bit too chaotic and dissonant) complements Mori's disorienting electronic noise with Sylvie Courvoisier on prepared piano and Ned Rothenberg on woodwinds, saxophone, shakuhachi, clarinet and bass clarinet. The jazz element prevails in the almost intangible Beauty In Disarray, thanks to Satoko Fujii's piano and Natsuki Tamura's trumpet. There are also an ethereal duet with cellist Erik Friedlander, Falling Blue; a brutal duet with Zeena Parkins's harp, Outburst; a noisy and ominous duet with Charmaine Lee (vocal sounds and electronics), Down Below; and a tenuous droning duet with David Watson's bagpipes, Dusk To Dawn. Mori never abandoned her mission of noise terrorist, but had become a soundsculptor and conductor of electroacoustic chamber music.

Phantom Orchard returned with Hit Parade Of Tears (Tzadik, 2024), inspired by the short stories of Izumi Suzuki, on which Zeena Parkins plays acoustic and electric harp, electronics, percussion, harmonium, synth and accordion, and Ikue Mori plays electronics, small percussion and processing.