The following season, Rypien made the Canucks' line-up out of training camp for the first time in his career. After scoring two goals in the first five games in 2008–09, he suffered a sports hernia in October. Upon recovering, he was granted an indefinite leave of absence for personal reasons. The Canucks organization alluded to Rypien's history of injuries as the main reason for him not returning to the team. Assistant general manager Lorne Henning stated that "It's just wearing on him now - it's frustrating for him. He just has to deal with the injuries … and wrap his head around it." It was later made known, following his death, that Rypien was struggling with clinical depression. He returned after a 70-game absence on March 31, 2009, in a contest against the Minnesota Wild. He appeared in 12 games for the Canucks in 2008–09, recording three goals and no assists. The season marked Vancouver's return to the playoffs after failing to qualify the previous season. After eliminating the St. Louis Blues in the first round, they were defeated in six games by the Chicago Blackhawks. Rypien appeared in all ten Canucks playoff games and recorded two points (both assists) while playing on the fourth-line alongside Darcy Hordichuk and Ryan Johnson. He recorded his first playoff point in Game 4 of the second round against Chicago, assisting on a Hordichuk goal with a spin-o-rama pass.