MacIntyre often told people he was orphaned by a Scottish family and raised in an Australian orphanage and a child labor camp.He used the aliases Paul Grant Jeffery, Timothy/Tim C. Allen, Oleg V. Bredikhine, and the nickname Froggy.

In 2000, MacIntyre was arrested after a neighbor said he duct-taped her to a chair, shaved her head, and painted her black. He wound up pleading guilty to third-degree misdemeanor assault.

On June 24, 2010, he was removed from his apartment by police and taken to Coney Island Hospital for evaluation after sending a despondent email to friends, one of whom called 911. He was released hours later, and returned home, where he lit his apartment in a crowded apartment building on fire. The fire "grew quickly into an “all-hands” blaze that took 12 trucks and 60 firefighters more than an hour to extinguish" but thankfully no other residents of the building were killed.

Although MacIntyre professionally published many works of non-fiction and literature, he is best known as an author of genre fiction: specifically, science fiction, fantasy, horror, and mystery stories. His short stories were published in Weird Tales, Analog, Asimov's Science Fiction, Amazing Stories, Absolute Magnitude, Interzone, the Strand Magazine, and numerous anthologies, including Terry Carr's Best Science Fiction of the Year #10 Contents Lists, Michael Reaves and John Pelan's mystery/horror anthology Shadows Over Baker Street, James Robert Smith and Stephen Mark Rainey's horror anthology Evermore, and Stephen Jones's The Mammoth Book of Best New Horror. For Mike Ashley's The Mammoth Book of Historical Detectives, MacIntyre wrote "Death in the Dawntime," a locked room mystery (or rather, sealed cave mystery) set in Australia around 35,000 BC, which Ashley suggests is the furthest in the past a historical whodunnit has been set.

In addition to publishing science fiction in Analog, MacIntyre also contributed to that magazine as an artist, illustrating his own stories and some by Ron Goulart. MacIntyre also published stories in the Russian-language science fiction magazine Esli.

A characteristic of MacIntyre's writing (both fiction and non-fiction) is his penchant for coining new words and resurrecting obscure words. Language authority William Safire had acknowledged MacIntyre's neologisms.

From October 2002 through November 2005, MacIntyre was a regular contributor to the “Big Town” feature of the New York Daily News, publishing more than 30 by-lined articles about Broadway musicals, restaurants, songwriters, athletes, and other figures in New York City's history. The May 2, 2007 issue of the New York Press carried his first by-lined article for that paper.

MacIntyre wrote a considerable number of book reviews for The Magazine of Fantasy & Science Fiction. In the July 2003 issue of that magazine, MacIntyre mentioned that he was related to the wife of Scottish author Eric Linklater. This admission is significant, as MacIntyre had stated (in interviews and at science-fiction conventions) that he was estranged from his abusive family and did not acknowledge them. He had legally changed his name, officially filing a deed poll: "Fergus MacIntyre" was therefore his legal name but not his birth name. He had acknowledged that he took the name "Gwynplaine" from the protagonist of The Man Who Laughs, a novel by Victor Hugo.

As a screenwriter, MacIntyre contributed substantial script material to a 2006 documentary about actress Theda Bara, The Woman with the Hungry Eyes: his contributions included the film's title and an interview he had conducted with author Fritz Leiber. Contractually prevented from receiving a screenplay by-line, MacIntyre received "special thanks" in the film's credits.

MacIntyre reportedly worked extensively as a ghost writer, most notably contributing to Jerzy Kosinski's Pinball..

Books

Novels and collections include:

• The Woman Between the Worlds (1994, ISBN 0-440-50327-2 and 2000, ISBN 0595088848)
• MacIntyre's Improbable Bestiary (2005, ISBN 1587154722)

Short stories

Short stories include:

• Asimov's Science Fiction:
• "For Cheddar or Worse" (volume 4 number 11, November 1980)
• "Martian Walkabout" (volume 5 number 13, December 1981)
• "Isle Be Seeing You" (volume 6 number 4, April 1982)

• Amazing Stories:
• "The Man Who Split in Twain" (May 1986)

• Weird Tales:
• "The Ones Who Turn Invisible" (#293, 1988)
• "Beddy-Bye" (Summer, 1998)

• Absolute Magnitude:
• "The Minds Who Jumped" (Spring 1995)

• Albedo One, (Ireland):
• "An Actor Prepares" (#20, 1999)

• Analog Science Fiction and Fact:
• "OOPS!" (March 1991)
• "Teeny-Tiny Techno-Tactics" (March 1997)
• "Time Lines" (June 1999)
• "A Real Bang-Up Job" (July 2000)
• "'Put Back That Universe!'" (October 2000)
• "Schrödinger's Cat-Sitter" (July 2001)
• "A Deadly Medley of Smedley" (April 2003)
• "Annual Annular Annals" (January 2004)

• Interzone, (Britain):
• "Sundowner Sheila" (February 2006)

• Strand Magazine:
• "Down the Garden Path" (February 2008)

• Esli, (Russia):
• "Random" (July 2008)
• "Smart Fashions" (June 2009; cover story)
• "Boarder Incidence" (February 2010)

• Space and Time Magazine:
• "Another Fine Messiah" (#110, Spring 2010)

• SF Magajin, (Japan):
• "The Adventure of Exham Priory" (May 2010)