Billy Eppler’s resignation from the Mets came amid an MLB investigation

The Mets’ new era of hope began with a dash of familiar chaos.

In a startling development, Billy Eppler on Thursday resigned as general manager of the Mets amid an ongoing Major League Baseball investigation into alleged improper uses of the injured list during the 2023 season, The Post has learned.

MLB confirmed the investigation, but not its nature, to The Post.

MLB was notified via anonymous letter of the IL’s alleged violations, according to a source.

A source said MLB plans to interview several Mets employees as part of the investigation.

It was not immediately clear whether the Mets might face any type of punishment.

When MLB informed the Mets of the investigation, Eppler decided to resign rather than become a distraction for David Stearns’ new management.

Eppler had not yet spoken with MLB officials as of Thursday night, but is expected to cooperate with that investigation, sources said.

Stashing healthy players on the IL can help a team compete. Classifying healthy players as injured can enable clubs to keep these players under team control rather than risk losing them to other organisations.

Eppler resigned three days after attending a news conference introducing Stearns, the new president of baseball operations, who said he “looks forward to working with” Eppler.

Instead, the Mets’ leader over the past two seasons will not see a third season.

“I wanted David to have a clean record, and that means stepping down,” Eppler said in a statement released by the Mets. “I wish nothing but the best for the entire Mets organization.”

Eppler declined to comment further.

Stearns was not quoted in the press release. Owner Steve Cohen thanked the former head of his front office.

“Billy Eppler led this team through a 101-win season and the postseason last year and we will miss him,” Cohen said in the statement. “We accepted Billy’s resignation today because he decided it was in everyone’s best interest to turn over complete leadership of baseball operations to David Stearns. On behalf of the Mets organization, we wish him the best.”

The GM’s resignation marked another unceremonious exit for a Mets official.

Before team leader Sandy Alderson stepped down and became a special counsel in early 2023, Cohen helped hire Eppler and said “the vetting process was broader and deeper than any we’ve ever had” for past mistakes.

Eppler’s immediate predecessors were Jared Porter and Zach Scott, who were both fired for off-field issues.

In January 2021, it was discovered that Porter had previously sexually harassed a female journalist while working for the Cubs.

Scott took over and became acting general manager until September 2021, when he was arrested on a drink-driving charge of which he was later acquitted.

Before Porter and Scott there was Mickey Callaway, the Mets’ manager from 2018-2019.

In 2021, he was suspended and placed on MLB’s ineligible list for sending inappropriate messages and photos to female reporters.

Amid the revolving door in Queens stepped Eppler, who was hired in November 2021 as general manager after a lengthy search for a president of baseball operations that came vacant.

He impressed early and led an organization that bet well on free agents and acquired Max Scherzer, assembling an excellent team in 2022 that was eliminated from the wild-card round.

This season was a much bigger struggle and culminated with the trade deadline sell-off in which Scherzer and Justin Verlander, among others, were sold while the Mets rebuilt their farm system.

Eppler has been particularly praised for his strength in the international market, having successfully landed Shohei Ohtani when he was with the Angels and Kodai Senga with the Mets.

He won’t be around during the offseason when Ohtani is a free agent and Japanese right-hander Yoshinobu Yamamoto will hit the open market.

Once Eppler was appointed, it was known that Cohen would eventually appoint someone above him.

Publicly, Eppler has always been OK with serving as a general manager under the president of baseball operations, and as recently as Monday, the Mets spoke as if they expected Eppler to be part of their future.

“Billy and I have had a really nice relationship for years as competitors,” Stearns said Monday. “Talking to each other whether it’s transactional or industry events. I have great respect for the experience he has in this game, the experience he has in New York and I look forward to working with him.”

Cohen has stated that he wants the front office to be as deep as possible.

“My goal is to build management talent in this organization,” Cohen said. “Baseball operations are very complex. There are a lot of moving parts. Building a strong management team is paramount to me.