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Through his association with Cibo Matto, he was approached by the Beastie Boys' Adam Yauch, who expressed an interest in Sean's music. His debut solo album, Into the Sun, was released in 1998 on the Beastie Boys' record label, Grand Royal Records, and garnered positive reviews. Regarding Grand Royal, Sean has said, 'I think I found the only label on the planet who doesn't care who my parents are and what my name is. It's a good feeling to know that I wouldn't have gotten the offer if they wouldn't have liked my songs. That's pretty rare in the music business!' A music video for "Home", one of the album's tracks, was directed by Spike Jonze.

In 1999, Sean's EP Half Horse, Half Musician - compilation of outtakes and remixes from Into The Sun - was released; the Japanese version contained the bonus track "Into the Sun (Moog Remix)". He also made a guest appearance on the underground, hip-hop collaborations,, Deltron 3030, working with Del Tha Funkee Homosapien and Dan Nakamura, singing the bridge to the song "Memory Loss".

He has also appeared on records by Handsome Boy Modeling School, Money Mark, and Ben Lee, and with musicians such as Josh Haden. He provided an introduction to a song on the Jurassic 5 album Quality Control. Past girlfriends include Yuka Honda (of Cibo Matto with whom he lived from 1996 to 1999), Bijou Phillips, Leelee Sobieski, and Elizabeth Jagger (daughter of Mick Jagger).

After Grand Royal Records' demise in 2001, Sean signed with Capitol Records, yet no material surfaced until early February 2006 on his website. A song called "Dead Meat" is to be his first single (with a video recorded and scheduled to be released) from his new album Friendly Fire. The new album will be released in October 2006 on Capitol Records.