Ahead of the 2012–13 season Murphy suffered a cruciate ligament injury, which kept him out for most of the season. At the same time a hamstring injury sidelined O'Donohoe. In their absence, academy scrum-half Kieran Marmion excelled, and went on to start every game that season. Murphy mad only a single substitute appearance that season, coming in the 2012–13 Pro12.