Dwyer is best known for his work on Captain America vol. 1 (1987—1990), Danger Unlimited (on the Torch of Liberty story) (1994), Action Comics (1995—1996), Avengers (vol. 3) (2001—2003) and his creator-owned series, LCD.

2000, he was sued by Starbucks Coffee for parodying their famous siren logo on the first cover of his comic book series LCD: Lowest Comic Denominator and also putting the image on t-shirts and stickers that he sold on his website and at comic book conventions. With assistance from the Comic Book Legal Defense Fund, the two parties settled the case out of court. The settlement established that the image was protected speech, citing the "parody" exception in Constitutional law; however, Dwyer is no longer allowed to use the image for financial gain because of its "confusing similarity" to the original material. Nevertheless, the image can be found on many other websites.

LCD: Lowest Comic Denominator had 2 "ashcan" editions, #1 (1997) and #2 (1998), before coming out with full comic versions starting a year later with #0 (a 2nd print was later issued with pieces removed due to the Starbucks legal action), 1, 2, and 3.

Most recently, Dwyer has been collaborating with Rick Remender on a number of titles, including XXXombies (the first in a planned line of horror comics Crawl Space), Sea of Red and Night Mary.

Dwyer was once the stepson of fellow comics creator John Byrne (with whom he collaborated on the Torch of Liberty strip) for a period when Byrne was married to Dwyer's mother.

He lives in Portland, Oregon, where he is a member of Periscope Studio.

Comics work includes:

• Batman #413 (with Jo Duffy, DC Comics, November 1987)
• Classic X-Men #17-29 (with Chris Claremont, Marvel Comics, January 1988 - January 1989)
• Captain America#338-367 (with Mark Gruenwald, Marvel Comics, February 1988 - February 1990)
• Batman #452-454 (with Peter Milligan, DC Comics, August—September 1990)
• Daredevil #289-290 (with Ann Nocenti, Marvel Comics, February—March 1991)
• Action Comics #671 (with Roger L. Stern, DC Comics, November 1991)
• Danger Unlimited: "Torch of Liberty" (with John Byrne, Legend/Dark Horse Comics, February—May 1994)
• Action Comics #712-721 (with David Michelinie, DC Comics, August 1995 - May 1996)

• The Avengers #48-50, 53-54, 57-60 (with Kurt Busiek and Geoff Johns, Marvel Comics, January 2002 - January 2003)
• Remains (with Steve Niles, 5-issue limited series, IDW Publishing, May—September, 2004)
• Sea of Red #3-13 (script, with co-author Rick Remender, Image Comics, May 2005 - November 2006)
• Night Mary (script and art, with co-author Rick Remender, 4-issue mini-series, IDW Publishing, July—November 2005)
• XXXombies (with Rick Remender, 4-issue mini-series, Image Comics, October 2007 - February 2008)
• Fear Agent #20-21 (with Rick Remender, Dark Horse Comics, April—June 2008)