After returning from the Euro 2008, Mertesacker again missed the beginning of the new season with a knee injury and through illness. In September, he returned to the starting line-up. He scored the opening goal in the DFB-Pokal semi-final away at northern rivals Hamburger SV to break the deadlock after a goalless first half, but the home side equalised, forcing the match into extra time and Bremen eventually triumphed 4–2 on penalties. He was ever present for the rest of the season until injury forced him off in the UEFA Cup semifinal second leg against Bundesliga rivals Hamburg. It was later revealed that he had torn ligaments in his right ankle and required surgery. He was ruled out for the rest of the season, as well as the UEFA Cup final loss against Shakhtar Donetsk and DFB-Pokal final, which they won. He scored four goals in all competitions, including a crucial equalizer against VfL Wolfsburg.