Mets owner Steve Cohen and former GM Billy Eppler reportedly...

Mets owner Steve Cohen and former GM Billy Eppler reportedly have the eye of Major League Baseball.  Credit: Jim McIsaac; Jeff Bachner

Major League Baseball has told the Mets that it is not targeting owner Steve Cohen in its investigation into the team’s potential misuse of the injured list, a source said Friday night.

That came after a New York Times report published Friday afternoon said MLB was looking into what Cohen, a hedge-fund multibillionaire, knew or should have known after an anonymous letter sent to the commissioner’s office included allegations that the Mets broke rules regarding the IL.

The investigation is ongoing, a source said.

After the Mets learned of its existence Thursday, Billy Eppler stepped down as general manager, an unanticipated twist after Cohen indicated Monday that Eppler would stay on under new president of baseball operations David Stearns — another episode in an unusually busy first week of the offseason, even by the Mets’ standards.

The letter, sent to the league within the past two weeks, according to the Times, said the Mets had put at least one healthy player on the IL.

Although it is illegal, it is normal for teams to use the so-called phantom IL as a way to stash players they otherwise would be at risk of losing. If a player is struggling and the club wants to give him a chance to straighten out — or if a roster spot is needed for somebody better — the player will be moved to the injured list, sometimes with an ambiguous injury, instead of being cut outright.

The Mets in 2023 had 25 players spend a total of 1,611 days on the IL, according to Spotrac, a website that tracks such statistics. They ranked 11th out of 30 in the first category, 13th in the second.

Part of MLB’s motivation in looking at the Mets and Eppler, the Times said, is to prove that it takes allegations of cheating seriously. The league plans to examine cellphone data, text messages and emails, and medical records as well as talk to players, front-office people and athletic training/medical personnel.

The Times also said the letter contained other accusations about Eppler’s conduct as GM, but the report did not specify what. It did say that Cohen has cooperated with the investigation.

Eppler was the Mets’ GM for two seasons. At Stearns’ introductory news conference at the start of the week, Cohen praised Eppler, saying that with him and Stearns, “one and one equals three.” Stearns said he had “a really nice relationship” with Eppler through the years as competing executives. Then came a Thursday afternoon news release from the Mets, then word of an MLB investigation.

“I wanted David to have a clean slate and that meant me stepping down,” Eppler said in a statement put out by the team.

Cohen said: “We accepted Billy’s resignation today as he decided it is in everyone’s best interest to fully hand over the leadership of baseball operations to David Stearns. On behalf of the Mets organization, we wish him all the best.”

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