During the investigation, Watson was among the thirty-four present and former Essendon players issued show cause notices by ASADA and infraction notices by the AFL, alleging the use of the banned peptide Thymosin beta-4 during the 2012 season. On 31 March 2015, the AFL Anti-Doping Tribunal found all thirty-four players not guilty of all charges. In January 2016, following an appeal by WADA against the AFL Tribunal's not-guilty finding, Watson, along with the other thirty-three players, had their not-guilty verdict overturned. All thirty-four players were suspended for two years, backdated to November 2016, causing him to miss the entire 2016 AFL season.