Stewart is best known for his work on Catwoman with writer Ed Brubaker, numerous collaborations with writer Grant Morrison, including Batman and Robin, Seaguy, and Seven Soldiers: The Manhattan Guardian, and The Other Side, a miniseries about the Vietnam war (written by Jason Aaron), for which he travelled to Vietnam for research. The Other Side was nominated for an Eisner Award in the Best Limited Series category of 2007.
Other projects include The Apocalipstix published by Oni Press, written by Ray Fawkes, and 4 issues of the SuicideGirls comic book.
He illustrated issues 7-9 of Batman and Robin, a storyline entitled "Blackest Knight", written by Grant Morrison. He returned to Batman and Robin with issue #16, drawing the first half of Morrison's final issue.
In September 2009 he won the 2009 "Outstanding WebComic Creator/Creative Team" Shuster Award for Sin Titulo, a serialized long-form webcomic he writes and draws. Sin Titulo is a neo-noir mystery thriller with elements of autobiography. In July 2010 he won the 2010 "Best Digital Comic" Eisner Award for Sin Titulo.
Stewart wrote and drew the miniseries Assassin's Creed: The Fall, based on the Assassin's Creed video game series, in collaboration with fellow writer/artist Karl Kerschl.
Along with Kagan McLeod, Ben Shannon, Steven Murray, and Chip Zdarsky, he is a co-founder of the studio The Royal Academy of Illustration and Design. He is also a co-founder of the Transmission-X webcomics collective.
Stewart created drawings which appeared in a comic book-style animation sequence at the end of the music video for Canadian pop singer Skye Sweetnam's song "Human", the first single from her second album Sound Soldier.
In 2014, Stewart was announced as the new writer for DC's Batgirl after fan favorite Gail Simone departs the title in October 2014. He will be joined by co-writer Brenden Fletcher, artist Babs Tarr, and colorist Jordie Bellaire.
He drew The Multiversity: Thunderworld Adventures (Feb. 2015), the fifth issue of Grant Morrison's The Multiversity project.
Stewart is currently illustrating the sequel to Fight Club, which is written by the novel's author Chuck Palahniuk and published as an ongoing 8-Part series by Dark Horse Comics in 2015.