Mets general manager Billy Eppler speaks at a news conference at...

Mets general manager Billy Eppler speaks at a news conference at Citi Field on Dec. 19, 2022. Credit: Corey Sipkin

The Mets’ hoped-for new era of stability and success is off to a weird start.

Billy Eppler suddenly resigned as general manager, the Mets announced late Thursday afternoon, amid what a source confirmed is an MLB investigation into him — three days after owner Steve Cohen described him as a significant part of the front office even in the face of his demotion.

The investigation began this week, the source said. It involves the potential misuse of the injured list, the New York Post reported.

The Mets had several IL transactions this season that seemed conveniently timed, creating an open roster spot just as the team needed one. On multiple occasions, then-manager Buck Showalter said he could come up with a reason to put any player — even ones who pitched or played with no ill effects the day before — on the IL.

In their news release, the Mets framed Eppler's departure as a selfless decision made by Eppler for the good of the organization.

“He decided it is in everyone’s best interest to fully hand over the leadership of baseball operations to David Stearns,” Cohen’s statement said in part. “On behalf of the Mets organization, we wish him all the best.”

Eppler’s statement read in whole: “I wanted David to have a clean slate and that meant me stepping down. I hope for nothing but the best for the entire Mets organization.”

Stearns, who started as president of baseball operations on Monday, was not quoted in the Mets’ three-paragraph announcement.

When the Mets fired Showalter last weekend, they offered to let him step down instead, he said, which he declined to do. It was not clear if Eppler’s decision came under similar circumstances.

Eppler did not respond to a request for comment.

Multiple upper-level Mets executives said they were caught off guard by Eppler’s departure.

At Stearns’ introductory news conference on Monday, Eppler — who retained his GM title but became the No. 2 baseball executive after two years of being No. 1 — sat in the front row.

Asked directly then whether Stearns had autonomy over Eppler’s status, as he was granted with Showalter, Cohen did not say yes, suggesting he wanted Eppler to remain.

“It’s my goal to build up the management talent in this organization,” Cohen said. “I mean, baseball operations are pretty complicated. There’s a lot of moving parts. And you know, building a strong management team is paramount to me. So I viewed it as one and one equals three.”

Stearns said that he and Eppler had a “really nice relationship going back years” as fellow executives. Eppler previously ran the Angels for five seasons beginning in late 2015, the same time Stearns became GM of the Brewers.

He didn’t have a straight answer on what Eppler’s role would look like under him.

“It’s going to take us weeks and months — not only with Billy but the entire front office — to truly understand what that breakdown of responsibilities will be and where we can all use our best skill sets to help the organization,” Stearns said. “We will have a better understanding of exactly how that works in the coming weeks of the new year.”

Cohen hired Eppler in November 2021, the end of a second GM search in as many offseasons, a stretch that included the Mets talking to and considering dozens of candidates.

By the end of the offseason, Eppler had brought on several executives from his Angels days — including Long Island native Jonathan Strangio as senior vice president of baseball operations and Steve Martone as special adviser to the GM — and remade the roster with the signings of Max Scherzer, Starling Marte, Mark Canha, Eduardo Escobar and others.

The Mets won 101 games in 2022, Eppler’s first season, but following a conservative approach at the trade deadline, the team blew the rest of what had been a 10 1⁄2-game lead in the NL East. Then they lost to the Padres in the Wild Card Series.

When the 2023 season became a huge mess, the Mets never presenting themselves as contenders, Eppler led a sell-off of some of their best players, including Scherzer and Justin Verlander, for prospects.

His efforts in “re-purposing” the Mets’ resources, as he preferred to call it, drew strong praise from Cohen.

“As you witnessed at the trade deadline," Cohen said at the time, "I think Billy did a phenomenal job."

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