 Stewart only played four further matches in the 2009 season; he suffered a knee injury in the Sea Eagles' round six victory over the South Sydney Rabbitohs and missed a great deal of football.He returned in round 25, just in time for Manly's charge to the finals; after the Sea eagles initially struggled without him on the field.Manly were eliminated in the first round of finals, going down 40-12 to the Melbourne Storm at Etihad Stadium despite finishing fifth at the end of the regular season.