Basel were third in the table, seven points behind new champions Zürich and one adrift of runners-up Young Boys. In the 2008–09 Swiss Cup, Basel advanced via Schötz, Bulle, Thun and Zurich to the semi-finals. But here they were stopped by YB. After a goalless 90 minutes and extra time, YB decided the penalty shoot-out 3–2 and advanced to the final to become runners-up, as Sion became cup winners. Derdiyok left the club at the end of the season. During his two and a half years with the team, Derdiyok played a total of 119 games for Basel scoring a total of 43 goals. 63 of these games were in the Swiss Super League, 11 in the Swiss Cup, 16 in the UEFA competitions (Champions League and UEFA Cup) and 29 were friendly games. He scored 17 goals in the domestic league, six in the cup, two in the European games and the other 16 were scored during the test games. Bayer Leverkusen On 28 May 2009, Bayer Leverkusen secured Derdiyok's signature, committing him to a four-year contract until 30 June 2013, after attracting major European clubs attention, including Galatasaray and some Serie A clubs, he finally joined his Swiss teammate Tranquillo Barnetta. Prior moving to Bayer 04 Leverkusen, Derdiyok was linked with joining English side Everton but he however rejected a move, stating he is adamant that he is eager to make a proposed summer switch to Leverkusen. Derdiyok made his debut in the DFB-Pokal on 31 July in a match against SV Babelsberg 03, he scored the winning goal in the 67th minute to make the score 1–0. On 8 August 2009, he scored his first goal in the league on his league debut in a 2–2 draw against Mainz 05. He replaced the long-term absentee Patrick Helmes in the starting lineup. His goals contributed to the fact that Bayer Leverkusen was ranked first after the first leg of this season. In the end, Bayer finished fourth this season, qualifying for the 2010–11 UEFA Europa League. During the 2009–10 season, Derdiyok scored 12 goals in 33 Bundesliga matches. In the first half of his second season, Derdiyok again war a regular in the starting lineup, but was increasingly used as a substitute in the second leg of this season. He played alternately with Stefan Kießling. On 14 August 2010, Derdiyok scored his first goal of 2010–11 season debut