He returned again in 1999 and played all but five games over the next six seasons.
 In 2000, his leadership qualities were recognised when he was awarded the co-captaincy of the club alongside Adrian Fletcher.
 During the Round 4 2001 Western Derby McManus displayed one of the most courageous acts seen in a derby when he ran back with the flight of the ball to take a mark, only to collide heavily with David Wirrpanda.
 His resilience was displayed when he continued to play after the collision and kicked the goal from the resulting free kick.
 He played his 100th game for Fremantle in the second last game of 2001, becoming only the fifth player to do so.

In 2005, however, his form fell away and he struggled for selection.
 Amid calls for his retirement or delisting, he played on and had one of his best everseasons in 2006, playing all 22 home and away games and all three finals.
In 2007, he was one of only five Fremantle players to play in all 22 matches.
 Despite this, the calls for retirement continued, especially as it became clear that Fremantle's 2008 season would not result in reaching the finals series.
 He even denied the rumours early in the season before announcing that his final game of AFL football would be in the Round 18 Western Derby at Subiaco Oval.

McManus played his final game of football on 2008-08-03 against the West Coast Eagles at Subiaco Oval in which the Dockers won by 33 points.
McManus received many tributes before and after the match and celebrated the closure of his career with a lap of honour around the oval before he was chaired from the ground by Matthew Pavlich and Ryan Crowley through an honour guard of past and present Fremantle players.
He returned again in 1999 and played all but five games over the next six seasons.  In 2000, his leadership qualities were recognised when he was awarded the co-captaincy of the club alongside Adrian Fletcher.  During the Round 4 2001 Western Derby McManus displayed one of the most courageous acts seen in a derby when he ran back with the flight of the ball to take a mark, only to collide heavily with David Wirrpanda.  His resilience was displayed when he continued to play after the collision and kicked the goal from the resulting free kick.  He played his 100th game for Fremantle in the second last game of 2001, becoming only the fifth player to do so.
In 2005, however, his form fell away and he struggled for selection.  Amid calls for his retirement or delisting, he played on and had one of his best everseasons in 2006, playing all 22 home and away games and all three finals. In 2007, he was one of only five Fremantle players to play in all 22 matches.  Despite this, the calls for retirement continued, especially as it became clear that Fremantle's 2008 season would not result in reaching the finals series.  He even denied the rumours early in the season before announcing that his final game of AFL football would be in the Round 18 Western Derby at Subiaco Oval.
McManus played his final game of football on 2008-08-03 against the West Coast Eagles at Subiaco Oval in which the Dockers won by 33 points. McManus received many tributes before and after the match and celebrated the closure of his career with a lap of honour around the oval before he was chaired from the ground by Matthew Pavlich and Ryan Crowley through an honour guard of past and present Fremantle players.
Shaun McManus