Boy Sets Fire left Victory for the major-label Wind-Up in 2002 and quickly released the Live for Today EP as an introduction. It featured four new tracks and two live recordings. Next, they entered the studio with producer Dave Fortman (12 Rods, Evanescence) to record their full-length Wind-Up debut. Tomorrow Come Today arrived in April 2003 and was a progression toward accessibility. However, the new direction didn't lessen Boy Sets Fire's fiery political convictions in the least. The album included an incendiary political rant on its inside flap, and its controversial lyrics rankled some religious groups. A limited version of Tomorrow Come Today was also released with an accompanying DVD of live material and behind-the-scenes footage. The band toured behind Tomorrow but, soon after the record's release, lost bassist Avery, whom they replaced with Rob Ehrenbrand.

Wind-Up turned out to be a bad fit for Boy Sets Fire, so in summer 2005 they signed with Equal Vision (Burning Heart in Europe), which issued Before the Eulogy that fall. Their solid and eclectic fourth full-length, Misery Index: Notes from the Plague Years, followed in March 2006. Unfortunately, however, the album turned out to be their last. By the end of July, the band announced they'd be calling it quits after some final shows via a message on their website. Soon after the announcement, though, Latshaw had an accident at his construction job and suffered a broken neck, collapsed lung, and two broken vertebrae. Boy Sets Fire finished up their scheduled European tour with their guitar tech filling in, but waited on setting final American dates; their final show together finally occurred in early June at Philadelphia's Trocadero Theatre. In 2010 a message appeared on the band's Facebook page announcing their reunion. A full-scale European tour followed in 2011, and in 2012 the band returned to the studio to record their fifth studio album, 2013's While a Nation Sleeps.