The late '90s saw Mantia appear on releases by Godflesh (Songs of Love and Hate, Love and Hate in Dub) and the instructional video Brain's Lessons: Shredding Repis On the Gnar Gnar Rad, which includes the Ostinato and the Up Down Technique. The video is shot to look like a home movie and includes many humorous moments including a sit down steak dinner with his parents right in the middle of Brain "shredding" on a toy drum set. Although silly at times, the video is extremely informative for drummers looking to learn the hard grooves he is known for.
In the early summer of 2006, after four warm-up dates in New York City, Mantia toured Europe with Guns N' Roses. On June 21, 2006 it was announced he was taking a break from the GN'R tour. In Brain's absence replacement drummer Frank Ferrer has been performing in most of the band's shows. In the Fall of 2006, Ferrer was promoted to an official member of the band, which fueled speculation that Mantia had resigned or been fired from Guns N' Roses. However, Axl Rose mentioned him "working on things for the band" during his fan-forum interviews in December 2008. In the liner notes for GN'R's 2008 album, Chinese Democracy, replacement drummer Frank Ferrer thanks Mantia, saying "[Frank Ferrer would like to thank]... Brain, God bless you and your family." Additionally, Rose is rumored to have briefly considered a rotating drummer line-up for the 2009-10 leg of the Chinese Democracy World Tour that would have seen Mantia playing the band's Chinese Democracy material while Ferrer played the band's classic material. Ultimately, Brain only ended up making a guest appearance at Guns N' Roses' House of Blues West Hollywood show on March 12, 2012 playing congas on "You're Crazy" and "Rocket Queen".
Since his hiatus from GN'R, Mantia has primarily been focused on music behind the scenes as a composer and producer. Though in 2013/14 Mantia did a stint of drumming with band The Crystal Method for their new record (on which he was featured). These performances included appearances on Jimmy Kimmel Live, and Last Call with Carson Daly 
In 2011, Mantia partnered with singer Melissa Reese to form “Brain and Melissa”, a composing team. The duo composed two game themes for Sony Playstation and several pieces of original music for Playstation HOME, Mod Nation and Twisted Metal X. They also scored the music for the Playstation video games Infamous Second Son and Infamous 2 which was nominated for “Outstanding Achievement in Original Composition” by the Academy of Interactive Arts and Sciences.
Brain and Melissa composed the music for the 2011 horror comedy film Detention. They have worked with music video director Joseph Kahn on several television commercials for NASCAR, Trust Bank, Seat, Qoros and Johnnie Walker Blue (showcasing the posthumous appearance by Bruce Lee).