In November 2005, after playing with the Sharks for more than five seasons, Stuart was traded (along with Marco Sturm and Wayne Primeau) to the Boston Bruins in exchange for Joe Thornton.

Boston general manager Peter Chiarelli cited his inability to agree on a new contract with Stuart, who was scheduled to become an unrestricted free agent at the end of the 2006–07 season, as a reason for the trade.

[3] On February 26, 2008, the Kings traded Stuart to the Detroit Red Wings in exchange for second- and fourth-round picks in the 2008 and 2009 NHL Entry Drafts, respectively.

On July 1, 2014, with the Sharks intent on getting younger, Stuart accepted a trade to provide a veteran presence to the Colorado Avalanche in exchange for second- and sixth-round picks in the 2016 and 2017 NHL Entry Drafts, respectively.

[12] During the subsequent off-season on June 27, 2016, with the Avalanche aiming to go younger on defence, Stuart was bought out from the remaining year of his contract, ending his tenure with Colorado.