In 2008 he made a comeback to rowing after leaving the sport after the 2000 Sydney Olympics, in pursuit of a sailing career as a grinder. With 8 years out of the sport he broke the 2000 m and 5000 m world records on the rowing machine and defeated Mahé Drysdale, the world champion in the single sculls, who was also a New Zealander. As it was an Olympic year and only one crew can be sent to the Olympics in each boat class the stage was set for a battle to see who would fill the Olympic single sculls spot. Despite Waddell getting the better of Drysdale in the domestic regattas the selectors created a three-race trial to decide who would go. With the wins for each sculler tied at 1–1 it came down to a final race which Drysdale won.