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McGerr joined the Bellingham, Washington-based indie rock band Death Cab for Cutie in early 2003, to replace drummer Michael Schorr. Two members of the band, Ben Gibbard and Nick Harmer, had previously played in Eureka Farm, where McGerr was Gibbard's replacement. McGerr debuted on Death Cab for Cutie's fourth album, Transatlanticism, released in October 2003, featuring two songs co-written by McGerr. The release of Transatlanticism to critical acclaim and strong commercial performance (and eventual gold certification by the Recording Industry Association of America) brought Death Cab for Cutie mainstream success. Speaking in 2003, Benjamin Gibbard notes that he "definitely believe[s] this will be the last drummer we'll ever have. It's kind of come full circle. It makes more sense having him than it has anyone else that's ever played with us."
Mc Gerr was a guest performer on Tegan and Sara's album The Con, released in July 2007, and can be seen recording in studio with them on the DVD entitled The Con DVD by Tegan and Sara. He also played drums for their next album, Sainthood, released in October 2009. McGerr played drums on half of the tracks on Matt Nathanson's 2007 album, Some Mad Hope, and was a guest drummer on Nathanson's 2009 album, Modern Love. McGerr also performed drums on three songs for his Death Cab for Cutie bandmate Chris Walla's debut solo album, Field Manual, released in 2008.