The first time he and brother Brett played together in first grade was in Round 18 of the 2004 season when the Sea Eagles defeated the Wests Tigers 26–18 at the home of Manly, Brookvale Oval on 11 July.

Between 2003 and 2006, Stewart only played 19 games for the Sea Eagles, often finding himself in their NSW Cup side due to the presence of established back rowers Ben Kennedy, Anthony Watmough, Luke Williamson, and Manly club legend Steve Menzies.

With Kennedy's retirement from playing at the end of the 2006 NRL season, coach Des Hasler gave "Gifty" his chance to cement a first grade place in the team from 2007.

Early in the second half of the Grand Final, his brother Brett was knocked out in a legal tackle by the Storm's Michael Crocker and Billy Slater while attempting to catch a mid-field bomb.

[9] Stewart was one of five Manly players selected, the others being front rowers Brent Kite and Josh Perry, Anthony Watmough and rookie winger David Williams.

Brett Stewart, who was in superlative form for Manly during the second half of the season and through the finals (ending the year as the NRL's leading try scorer with 22), was originally selected but was forced to withdraw with a shoulder injury.

With less than one minute to go before half time, Stewart put in a grubber kick on his own 20m line for Manly winger Michael Robertson who regathered and raced 35m upfield before passing inside to hooker Matt Ballin who was then tackled only 5m from scoring a try.

The resulting play saw halfback (and the NRL's Dally M Rookie of the Year) Daly Cherry-Evans score beside the posts to give Manly a 12-2 and ultimately winning lead going into half time.