During 2366, Duffy assisted with transporting tissue samples from the Mikulaks into cargo bay 5 along with Miles O'Brien. Unfortunately, he was accidentally contaminated with invidium and subsequently spread this element throughout several ship's systems. During the trip, he was assigned to realign the magnetic capacitors in the matter/antimatter injectors, together with his colleague Costa. While drinking a beer in Ten Forward, he contaminated his glass with the invidium and thereby changed its molecular structure, causing it to leak. After discussion with the senior engineering officers, he realized what happened to him. He underwent bio-decontamination on Starbase 121 with several other officers. (TNG: "Hollow Pursuits")
In Pocket Books non-canon Star Trek: Starfleet Corps of Engineers series, Duffy appears (in the post-Dominion War era) as the second officer of the series' ship, USS da Vinci, rank of lieutenant commander. In the books, his first name is Kieran, which coincidentally is also MacDuff's first name. He is also said have had a past relationship with da Vinci first officer Sonya Gomez when they both served aboard the Enterprise. When the da Vinci became trapped in the gas giant, Galvan IV, Duffy gave his life to complete his mission and ensure the safety of his crewmates.