As a young boy, O'Mahony would write his own stories based on Doctor Who, and pitched ideas to the BBC for episodes of the show. At the age of 12, he wrote to Nigel Robinson — the then editor of Target Books — demanding to be allowed to write the novelization of the television story "The Daleks' Master Plan". The request wasn't granted, although it did take several years for Target's successors, Virgin Publishing, to negotiate the rights to novelise the story.
Following the announcement of Virgin's intention to start publishing the New Adventures, O'Mahony submitted a number of proposals for novels, the third of which (Falls the Shadow) was accepted and published in November 1994. This was the only book that O'Mahony wrote for the New Adventures, however in July 1994 Virgin began publishing the Virgin Missing Adventures, and O'Mahony pitched a novel for this series and was accepted. The novel, The Man in the Velvet Mask was published in February 1996.
O'Mahony did not write any novels for BBC Books' Past Doctor Adventures and Eighth Doctor Adventures ranges, however he did write two short stories for their Short Trips anthologies. One story was "Nothing at the End of the Lane," in Short Trips and Side Steps in March 2000. ("Nothing at the End of the Lane" was originally the title of an unused idea for the first episode of Doctor Who and has also been used by a magazine about the recovery and restoration of archive Doctor Who episodes, unrelated to the "Short Trips" story.)
In June 2003, O'Mahony wrote the novella The Cabinet of Light for Telos Publishing Ltd. as part of their range of Doctor Who novellas. The novella created the characters of Honoré Lechasseur and Emily Blandish who went on to star in Telos' Time Hunter range of novellas, loosely connected to Doctor Who. O'Mahony followed this up in 2004 with the sixth installment in the popular Kaldor City series, Storm Mine which to date is the final installment of that series. He has also written the audio dramas Timeless Passages and The Tub Full of Cats for Big Finish Productions's Bernice Summerfield series.