On April 28, 2007 in a 3–2 win over the Dodgers, Hoffman earned a save and pitched in his 803rd game for the Padres, breaking the MLB record for games pitched for one team. The record was previously held by both Walter Johnson of the Washington Senators and Elroy Face of the Pittsburgh Pirates. On June 6 against the Dodgers, Hoffman became the first pitcher in MLB history to log 500 saves after the Padres' 5–2 victory. Hoffman was awarded the MLB Delivery Man of the Month for May after converting all 11 of his save opportunities and allowing no earned runs in 13 games. On July 1, Hoffman was named to the NL All-Star Team for the sixth time in his career. On September 8 against the Colorado Rockies, Hoffman struck-out Todd Helton swinging on a 74-mph change-up for his 1,000th career strikeout, becoming the eighth reliever to reach the mark. On September 27, Hoffman picked up his 40th save of the 2007 season, marking his ninth season with 40 saves, a Major League record. On September 29, one strike away from clinching the Padres third consecutive playoff berth, Hoffman surrendered a tying, two-out triple in the ninth inning to Tony Gwynn, Jr., son of legendary Padres Hall of Famer Tony Gwynn. The Padres would lose 4–3 in the 11th inning to the Milwaukee Brewers. On October 1, in the Padres' wild card tie-breaker game against the Rockies, Hoffman blew his second straight save opportunity and his team's 8–6 lead in the 13th inning. He took the loss when he allowed the game-winning run to score on a sacrifice fly. For the season, he converted 42 saves in 49 opportunities while posting a 4-5 mark and 2.98 ERA. His 42 saves were the third most in the NL. A couple of weeks after the end of the season, Hoffman had minor arthroscopic surgery on his pitching elbow to remove bone chips. He said it was unrelated to his pitching performance at the end of the season.
Hoffman surrendered a home run but recorded his 550th save on August 14, 2008 in a 3–2 victory over the Brewers. On September 19, 2008, Hoffman finished an 11–6 14-inning win over the Washington Nationals for his 900th career MLB game. Hoffman's 30th and last save of the season, a 3–2 win over the Pirates, ensured the Padres would not lose 100 games that season. The Padres finished with a 63–99 record after being projected by the team and analysts to win 87–90 games. Hoffman ended the 2008 season 3–6 with a 3.77 ERA and 30 in 34 save opportunities. He tied for sixth in the NL in saves. Hoffman reached 20 or more saves for the 14th time to set a new MLB record. His 13th 30-save season extended his MLB record. He had a 5.14 ERA through his first 29 appearances and a 1.56 ERA in his last 19 appearances of the season.
Hoffman, eligible for free agency, realized he was decreasing his leverage when he declared he wanted to return to play for San Diego in 2009 did not want to move his family. It was announced on November 10, 2008, that Hoffman would not return to San Diego in 2009. With his struggles during the season, the Padres lowballed a $4 million offer with an option for 2010 and later retracted that, ending his career with the Padres. It was not an amicable parting for Hoffman, who was the face of the franchise after Tony Gwynn's retirement following the 2001 season. His 902 career appearances as a Padre extended his own MLB record for games pitched with one team.
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