Doherty's work over a 15-year career has mainly been concentrated on the classic 2000 AD character Judge Dredd. He has illustrated several significant episodes of the strip. These include the story that has been acclaimed by fans as the best single episode story in the history of the strip,^{[citation needed]} "Bury My Knee At Wounded Heart"; the classic origins story "Judge Death: Boyhood of a Superfiend"; and the swansong story of long-running support cast member Chief Judge McGruder, "Death of a Legend."

Outside 2000 AD, Doherty's work includes Grendel Tales and Shaolin Cowboy.

Doherty is currently working on Devlin Waugh and the works of the Millarworld.

Comics work (pencils and inks, unless specified) includes:

• "Felicity" (with Chris Standley, in Crisis #47, 1990)
• "Young Death" (with John Wagner, in Judge Dredd Megazine vol.1 #1–12, 1990–1991, collected in Young Death: Boyhood of a Superfiend, May 2008, ISBN 1-905437-65-X)
• Judge Dredd:
  • "Justice One" (with Garth Ennis, in 2000 AD #766–771, 1992)
  • "Judgement Day" (with Garth Ennis, in 2000 AD #786–799, 1992, collected in Judgement Day, Hamlyn, 1999, ISBN 0-600-59970-1, Rebellion, 2004, ISBN 1-904265-19-7)
  • "Mechanismo Returns" (with John Wagner, in Judge Dredd Megazine vol.2 #22–26, 1993)
  • "Roadkill" (with John Smith, in 2000 AD #856–858, 1993)
  • "Bury My Knee at Wounded Heart" (with John Wagner, in Judge Dredd Megazine vol.2 #46, 1994)
  • "Mr Bennet joins the Judges" (with Mark Millar, in 2000 AD Sci-Fi Special 1994)
  • "Prologue" (with John Wagner, in Judge Dredd Megazine vol.2 #57, 1994)
  • "Moving Violation" (with Chris Standley, in 2000 AD #856–858, 1994)
  • "TV Babies" (with Chris Standley, in 2000 AD #898, 1994)
  • "Death of a Legend" (with John Wagner, in 2000 AD #1009, 1996)
  • "Spawney" (with John Wagner, in 2000 AD #1067–1068, 1996)
  • "Simp City" (with John Wagner, in 2000 AD #1119–1120, 1998)
  • "Dumskulls" (with Alan Grant, in 2000 AD #1171, 1998)
  • "Slow Crime Day" (with John Wagner, in 2000 AD #1191, 2000)
  • "The All New Adventures of P. J. Maybe" (with John Wagner, in 2000 AD #1204, 2000)
  • "Blow Out!" (with John Wagner, in 2000 AD #1213, 2000)
  • "Born Under a Bad Sign" (with Robbie Morrison, in 2000 AD #1275, 2002)
  • "Dead Lost in Mega-City One" (with John Wagner, in Judge Dredd Megazine vol.4 #9, 2002)
  • "Satan's Last Assault on Grud's Kingdom" (with Alan Grant, in 2000 AD #1288, 2002)
  • "A Right Royal Occasion" (with Gordon Rennie, in 2000 AD #1293, 2002)
  • "Versus" (with Simon Spurrier, in 2000AD #1499, 2006)
  • "Night School" (with John Wagner, in Judge Dredd Megazine #260, 2007)
  • "Mandroid: Instrument of War" (colours, with writer John Wagner and art by Carl Critchlow, in 2000 AD #1555–1566, 2007)
  • "Ratfink" (with John Wagner, in Judge Dredd Megazine #273–277, 2008)
  • "Old Wounds" (with John Smith, in Judge Dredd Megazine #287–288, August–September 2009)
  • "Grudsent" (with Simon Spurrier, in Judge Dredd Megazine #299, July 2010)
• Armitage: "City of the Dead Prologue" (with Dave Stone, in Judge Dredd Megazine #2.63, 1994)
• Grendel Tales: The Devil May Care (with writer Terry LaBan, 6-issue limited series, Dark Horse Comics, 1995, tpb 160 pages, 2003, ISBN 1-56971-796-6)
• The Dreaming #10–12, 17–19 (with Bryan Talbot and Caitlín R. Kiernan, Vertigo, 1997)
• Batman & Superman: World's Finest #6–8 (pencils, with writer Karl Kesel and inks by Robert Campanella, DC Comics, 1997, tpb, 2003, ISBN 1-4012-0082-6)
• Seaguy (colours, with writer Grant Morrison, and art by Cameron Stewart, 3-issue mini-series, Vertigo, 2004, tpb, 2005, ISBN 1-4012-0494-5))
• Breathing Space (with Rob Williams, in 2000AD #1451–1452, 2005)
• Shaolin Cowboy #1–7 (colours, with writer and artist Geof Darrow, Burlyman Entertainment, 2005–2007)
• Devlin Waugh: "Innocence & Experience" (with John Smith, in Judge Dredd Megazine #253–256, 2007)
• Millarworld:
  • MPH #1–4 (colours and letters, with writer Mark Millar, and art by Duncan Fegredo, Image Comics, 2014–2015, ISBN 1-6321-5265-7)
  • Empress #1–7 (colours, with writer Mark Millar, and art by Stuart Immonen, Icon Comics, 2016, ISBN 1-3029-0206-7)
  • Kingsman: The Red Diamond #1–6 (letters, with writer Rob Williams, and art by Simon Fraser, Image Comics, 2018, ISBN 1-5343-0509-2)
  • Chrononauts: Futureshock #1–4 (letters, with writer Mark Millar, and art by Eric Canete, Image Comics, 2019, ISBN 1-5343-1508-X)

2005: Nominated for "Best Colorist" Eisner Award, for Shaolin Cowboy^[1]

• Official page on Blogger
• 2006 Interview with 2000ADReview