Apple sang with Johnny Cash on a cover of Simon and Garfunkel's "Bridge over Troubled Water" that ended up on Cash's album American IV: The Man Comes Around and was nominated for a Grammy Award for "Best Country Collaboration with Vocals". She also collaborated with him on Cat Stevens's "Father and Son", which was included on Cash's 2003 collection Unearthed. Free Fiona campaigners outside the NYC headquarters of Sony BMG Music Entertainment in January 2005. Apple's third album, Extraordinary Machine, was originally produced by Jon Brion. Recording sessions began in 2002 at Ocean Way studios in Nashville, Tennessee, but later moved to the Paramour in Los Angeles. Work on the album continued until 2003, and in May of that year it was submitted to Sony executives. In 2004 and 2005 tracks were leaked on the Internet in MP3 format and played on U.S. and international radio; subsequently, MP3s of the entire album, believed to have been produced by Brion (although he later claimed the leaked tracks were "tweaked" beyond his own work), went online. Although a website distributing the album was quickly taken offline, they soon reached P2P networks and were downloaded by fans. A fan-led campaign, Free Fiona, was launched in support of the album's official release.

In August 2005, the album was given an October release date. Production had been largely redone by Mike Elizondo, who had previously played bass on Pawn, and co-produced by electronica experimentalist Brian Kehew. Spin later reported: "Fans erroneously thought that Apple's record label, Epic, had rejected the first version of Extraordinary Machine... in reality, according to Elizondo, Apple was unhappy with the results, and it was her decision to redo the record, not her label's". Two of the eleven previous leaked tracks were relatively unchanged, nine were completely retooled, and one new song was also included. According to Elizondo, "Everything was done from scratch". The final mastering of Extraordinary Machine was performed by Brian Gardner, the released version has a far higher level of compression than any of Fionas' previous releases.

Extraordinary Machine became the highest-charting album of Apple's career in the U.S. on its release (debuting at number seven) and was nominated for a Grammy Award for "Best Pop Vocal Album". It was eventually certified gold and sold 462,000 copies in the U.S.,, though its singles ("Parting Gift", "O' Sailor", "Not About Love" and "Get Him Back") failed to enter any Billboard charts. It was revealed in late 2005 that Sony was initially unhappy with the work, and Apple and Brion sought to rework the album. Sony reportedly made caveats on the process, to which Apple balked. After a long period of waiting, she began an attempt to rework the album with close friend Kehew. Elizondo was brought back as co-producer to complete the tracks he had begun with Brion and Apple. Despite suggestions that the album had caused a rift between Brion and Apple, they regularly perform together at Largo, a club in Los Angeles, including a joint appearance with Elizondo on bass just before the news broke of an official release. Apple went on a live tour to promote the album in late 2005, and from early 2006 supported Coldplay on their tour of North America.

• "Cold Case" (1 episode, 2008)
       - Spiders (2008) TV episode (performer: "Sleep To Dream")
• School for Scoundrels (2006) (writer: "Sleep to Dream") (performer: "Sleep to Dream")
• Fiona Apple: Extraordinary Machine (2005) (V) (writer: "Not About Love" (video),
  "Extraordinary Machine" (Live at Club Largo), "Paper Bag" (Live at Club Largo),
  "Fast as You Can" (Live at Club Largo), "Parting Gift" (Live at The Jazz Bakery))
• The Work of Director Mark Romanek (2005) (V) (performer: "Criminal")
• "Joan of Arcadia" (1 episode, 2004)
       - Jump (2004) TV episode (performer: "Across the Universe")
• "Daria" (3 episodes, 1997-2000)
       - Murder, She Snored (2000) TV episode (performer: "Fast As You Can")
       - A Tree Grows in Lawndale (2000) TV episode (writer: "Limp") (performer: "Limp")
       - The Misery Chick (1997) TV episode (performer: "Criminal")
• Pleasantville (1998) (performer: "Across the Universe")