Cooper is co-creator, along with Richard Case of Darkhold, part of the Marvel Comics universe. He also wrote a number of stories for Marvel Comics Presents, often featuring Ghost Rider and Vengeance. Cooper has also edited a number of X-Men collections.

In his work, in addition to usual motif and themes of the genre, he includes gay, lesbian and queer issues. For example he introduced the first gay male in Star Trek, Yoshi Mishima.

He was also a president of the Harvard Ornithological Club in the 1980s.

Comics work includes:

• Marvel Comics Presents:
• "Return of the Braineaters" (with pencils by John Stanisci and inks by Jimmy Palmiotti, in Marvel Comics Presents #107-112, Marvel Comics, 1992)
• "Siege of Darkness" (with pencils by Reggie Jones and inks by Fred Harper, in Marvel Comics Presents #144-146, Marvel Comics, 1993—1994)
• "Tower of Blood" (with pencils by Reggie Jones and inks by Fred Harper, in Marvel Comics Presents #147-148, Marvel Comics, 1994)
• "The Price" (with Fred Harper, in Marvel Comics Presents #149, Marvel Comics, 1994)
• "Dangerous Games" (with pencils by Reggie Jones and inks by Fred Harper, in Marvel Comics Presents #152-153, Marvel Comics, 1994)
• "Altered Spirits" (with pencils by Reggie Jones and inks by Fred Harper, in Marvel Comics Presents #156-157, Marvel Comics, 1994)
• "Final Gambit" (with pencils by Reggie Jones and inks by Fred Harper, in Marvel Comics Presents #175, Marvel Comics, 1995)

• Darkhold #1-16 (with Richard Case, Marvel Comics, 1992—1994)
• Excalibur #77-80 (Marvel Comics, 1994)
• Starfleet Academy #1-19 (with pencils by Chris Renaud and inks by Andy Lanning, Marvel Comics, 1996—1998)