In October 2018, Van Wagenen was appointed as the general manager of the New York Mets, a decision that surprised many in the baseball community due to his lack of direct front-office experience. His hiring marked a shift in the Mets' approach, as they opted for someone with a strong background in player representation rather than traditional team management.
During his tenure with the Mets, Van Wagenen made several bold moves. One of his first major transactions was the trade for All-Star second baseman Robinson Canó and closer Edwin Díaz from the Seattle Mariners. This trade was met with mixed reactions, as it involved sending top prospects Jarred Kelenic and Justin Dunn to Seattle. The deal highlighted Van Wagenen's willingness to take risks in an effort to improve the team's immediate prospects.
Van Wagenen also focused on bolstering the Mets' pitching staff. He signed free agent pitchers such as Marcus Stroman and extended the contract of ace Jacob deGrom, ensuring that the team's rotation remained competitive. Additionally, he worked on strengthening the bullpen by acquiring relievers like Dellin Betances.
Despite these efforts, the Mets faced challenges on the field. The team struggled to achieve consistent success, and their performance did not always reflect the ambitious moves made by Van Wagenen. The Mets finished the 2019 season with an 86-76 record, missing the playoffs. The following year, the COVID-19 pandemic shortened the MLB season, and the Mets ended with a 26-34 record.
Van Wagenen's time as general manager came to an end in November 2020, following the sale of the Mets to billionaire Steve Cohen. The new ownership decided to make changes to the front office, leading to Van Wagenen's departure. His tenure with the Mets was marked by a series of high-profile transactions and a focus on immediate competitiveness, though it ultimately did not result in postseason success.
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