Lieutenant (j.g.) Duffy joined the crew of the USS Enterprise-D in early 2364 during that ship's initial shakedown cruise. He was promoted to full Lieutenant in 2368. During his time on the Enterprise, he struck up a romantic relationship with Sonya Gomez. The relationship ended in 2368 when Gomez transferred to the USS Oberth.
By 2374, Duffy had been promoted to Lieutenant Commander, and was assigned to the Starfleet Corps of Engineers, serving aboard the USS da Vinci as second officer under Captain David Gold and Commander Salek. Following the death of Salek in 2376, Commander Gomez was assigned as his replacement, and was reunited with Duffy. After some initial uneasiness, they renewed their romantic relationship. A few months after, Duffy proposed marriage, but, before Gomez would give him her answer, the da Vinci found itself crippled within the atmosphere of gas giant planet Galvan VI. Duffy volunteered for the mission to save the ship, and was killed in the successful effort.
He was posthumously awarded the Federation Medal of Honor for his actions at Galvan VI.