Legal issues then saw Stewart suspended from the opening four rounds of the 2009 NRL season. Without Stewart at fullback, Manly opened their premiership defence with four straight losses. The rot stopped when Stewart returned in Round 5 against the Wests Tigers at Brookvale, scoring 3 tries as Manly won 23–10. He scored another two at Brookvale the next week against South Sydney before a knee injury forced him to miss the next 19 games. He made his return in Round 25 against Cronulla.