A classically trained violinist in his younger days, Nakamura instead fell in love with Kraftwerk and old-school hip-hop, as well as R&B and rock & roll. He began DJing as a teenager but was discouraged by the advanced skills of some younger Bay Area DJs (i.e., the ones who would go on to form the legendary Invisibl Skratch Piklz collective). Nakamura instead turned his attention to crafting his own productions, accepting gigs around the Bay Area through the early '90s, which eventually culminated in the Dr. Octagon project in 1995. A lo-fi fusion of hip-hop beats and bizarre atmospherics on par with some of the weirder exports from the U.K. trip-hop scene, Dr. Octagon was released by the tiny Bulk Recordings label in 1995 and achieved a level of overground success increasingly rare in hip-hop's pop-monopolized marketplace when it was reissued by DreamWorks a year later. Propelled by Thornton's pornographic rhymes and mind-bending meter, the record owed its success in equal measure to Nakamura's inventive production, which wed loping, downtempo rhythms with, by turns, weeping violins, space-born bleeps and wiggles, and heavy metal guitar riffs. Not Nakamura's freshman effort by a long shot, the two had actually worked together (with Thornton appearing as Sinister 6000) on Nakamura's debut Automator release, the Better Tomorrow EP, appearing on SF's Ubiquity label in early 1996. Nakamura's studio, The Glue Factory, also served as the workshop for recordings by Mo' Wax's DJ Shadow and for various artists on the latter's Solesides label (most notably on Latyrx's The Album).

When Thornton decided not to tour behind his Dr. Octagon alias, Nakamura racked up a host of other mix and production credits, including Primal Scream, the Eels, DJ Krush, a collaboration with Dust Brother Mike Simpson for Cornershop (several tracks on 1997's acclaimed When I Was Born for the 7th Time), and the Jon Spencer Blues Explosion (1998's Acme). Nakamura then teamed up with former De La Soul producer Prince Paul as Handsome Boy Modeling School, a reference to an episode of the Chris Elliott sitcom Get a Life. In 1999, the duo released an album titled So...How's Your Girl?, a freewheeling hodgepodge of old-school hip-hop, new-school trip-hop, crazed sampling (including plenty of Elliott dialogue), and all-star cameos. The record marked Nakamura as a figure to watch, and that reputation was confirmed with 2000's Deltron 3030 project, a collaboration with rapper Del tha Funkee Homosapien and DJ Kid Koala. The trio's self-titled debut was an elaborate science-fiction concept album set in a bleak and distant future, and Nakamura's detailed, cinematic production offered a rich and believable soundtrack. That same year, Nakamura issued a retooled version of his debut EP (with several extra tracks) under the title A Much Better Tomorrow on the hip-hop-oriented label 75 Ark.

In 2001, Nakamura snared his widest audience yet with the cartoon band Gorillaz, an eclectic collaboration with Blur's Damon Albarn, artist Jamie Hewlett, Cibo Matto's Miho Hatori, and former Talking Heads Chris Frantz and Tina Weymouth. Their barely classifiable self-titled debut was a hit on both sides of the Atlantic, going platinum in the U.S. and spawning Nakamura's first major hit single, "Clint Eastwood." Next, Nakamura returned to his Nathaniel Merriweather alias (from the Handsome Boy Modeling School album) for Lovage, a lounge-flavored, Serge Gainsbourg-influenced project that featured vocalists Jennifer Charles (Elysian Fields) and Mike Patton (Faith No More). The Lovage album Music to Make Love to Your Old Lady By was released before the end of 2001. Nakamura kicked off 2002 by releasing his first-ever mix album, the well-received Wanna Buy a Monkey?: A Mixtape Session.

Despite the fact there were many promises for a solo album, titled Omakase, label issues caused it to be shelved, but in 2004, the Automator teamed up with Daryl Palumba to form Head Automatica (at least in its initial conception) and release Decadence. In 2006, he produced the tracks for 2K7, the soundtrack to the video game of the same name, which featured performances from E-40, Ghostface Killah, and Slim Thug (though of course an instrumental version was also offered).