On January 6, 2003, the band began writing for their next record.
They were also featured on MuchMusic's "Celebrity Taste Maker" on January 24. Einziger, Kenney and Pasillas appeared at the Roxy Theatre on January 24 with Suzi Katayama and Time Lapse Consortium. The act, which featured an 11 piece orchestra, also included Neal Evans of Soulive. Suzi Katayama had worked with Incubus in the past on orchestral arrangements, specifically, in "Aqueous Transmission" and 2000s Almost Acoustic X-Mas performance. The show was the first performance of the group, which described its music as "an instrumental voyage into the world of psychedelic funk." On February 7, the band began renegotiations on their record contract.
The band, which had been signed to Epic/Immortal for seven years, cited the fact that state law limits the amount of time that an artist can be bound to a company. The band had been signed to the label for 7 years, and used California's "Seven Years Law" as a negotiating tool with Epic/Immortal. After releasing 3 highly successful albums, the band had been compensated poorly compared to the revenue that they had generated for Sony. The band entered a lawsuit against their label in order to break from their contract, to which Sony responded with a lawsuit of their own.
On March 1, Einziger, along with Scott Litt, Dave Holdredge, and Rick Will, was nominated for a Grammy in the "Best Engineered Album (Non Classical)" category, for their work on Morning View. On April 3, after weeks of circulating rumors about Alex Katunich's departure from the band, an official announcement was made by the band. A decision had been reached amongst members of Incubus in a face-to-face meeting at the end of the Morning View tour to discuss his involvement in the band. The band said that the split had become necessary due to "irreconcilable creative differences".
Almost immediately after the announcement of a new bass player, the 2003 Incubus v. Sony case had been settled. The two sides settled on a new contract that delivers three albums to Epic/Immortal with an option on a fourth. The first album would be worth $8 million in advances to the band, with another $2.5 million for each one thereafter.
In the summer of 2003, the band was booked to play the newly resurrected Lollapalooza circuit alongside Jane's Addiction, Audioslave, Jurassic 5, and Queens of the Stone Age. On this tour, they debuted two new songs, "Megalomaniac" and "Pistola". In October, the band released Live at Lollapalooza, whose proceeds went to their Make Yourself Foundation.
The album featured the song "Pistola", which hadn't been released at the time. After its release the band set out to play the 17th annual Bridge School Benefit on October 25 and 26th at the Shoreline Amphitheater in Mountain View, California. Neil Young organized the annual concert, which aides the Bridge School in its outreach to children with severe speech and physical impairments. Incubus performed the acoustic show along with Crosby, Stills, Nash and Young, Willie Nelson, Pearl Jam, Counting Crows, Wilco, Dashboard Confessional, and others. "A Crow Left of the Murder" and "Talk Shows on Mute" were debuted during the acoustic event.
By December the new album, produced by Brendan O'Brien (Pearl Jam, Soundgarden, Rage Against the Machine) was completed and scheduled for release. Titled A Crow Left of the Murder..., was to be an enhanced CD with behind-the-scenes video. In the videos, Einziger and Boyd discussed their new songs. Einziger described them as "like the old shit, but older. It's very different. It's very energetic and fast, and a lot of it is more technical. I guess maybe in the vein of more of our older songs; they don't sound like our older songs. They are more exploratory."
On December 15, the first single, "'Megalomaniac", was released. It raised controversy when it was said to be an attack on the Bush administration, and was banned from daytime view on MTV (despite the band saying that it was not an attack on a particular person, rather a comment on some people's negative attitudes). However, the band was actually pleased with this nighttime viewing restriction. Says Boyd, “When we heard our video had been relegated to late night rotation, I think that all of us were secretly like, ‘Yes!’ ”. Pasillas reflected Boyd's sentiments, saying, "I think it's okay if people think that we're trying to make a political statement. Whatever anyone conjures up or takes from our music is good; I mean, our point is to get people thinking."
A Crow Left of the Murder... was released in 2004, showcasing a new turn for the band. It combined the more experimental leanings of S.C.I.E.N.C.E. and Fungus Amongus with the mainstream rock of Make Yourself and Morning View.
The second single released was "Talk Shows on Mute", featuring a video that was inspired by George Orwell's 1984. After this release, Incubus hit the road again. As both "Talk Shows on Mute" and the earlier single, "Megalomaniac", reflect, Incubus' new album was a very politically oriented album. It reflected many of the band's political views, stressing critical thought, independence from the media, and nonviolence. Said Boyd during an interview in Lisbon, Portugal, "I think that the concept of war is archaic to a fault; it's completely outdated, and we need a new way of resolving dilemmas in the world."
Incubus toured worldwide in 2004 with many bands, including Ben Kweller, The Walkmen, Hundred Reasons, The Music, Brand New and Sparta, to promote their new album. One song left off the album, the 27-minute long instrumental entitled "The Odyssey", was later featured as in-game music and on soundtrack for the Xbox game Halo 2.
In November 2004, the band released a live DVD entitled Alive at Red Rocks, filmed in Red Rocks Park, Colorado, during their world tour for A Crow Left of the Murder.... Along with the DVD came a bonus CD featuring five tracks, including a studio version of live favorite "Pantomime", a movement from "The Odyssey" called "Follow", and the U.K. B-Side "Monuments and Melodies". Two live tracks were also included.
In December 2004, at a gig in Los Angeles the band played The Police hits "De Do Do Do De Da Da Da", "Message in a Bottle" & "Roxanne" with Stewart Copeland and Andy Summers from the former band. This follows performances of the songs at most shows throughout the fall.