As 2008 NRL premiers, the Manly Warringah Sea Eagles started their new season with the 2009 World Club Challenge match in England against Super League's 2008 champions, the Leeds Rhinos.
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.
Losses to two of the top three teams were the reasons for Manly's early exit, ending their premiership defence in disappointment.