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

In a stunning development, Billy Eppler resigned Thursday as Mets general manager amid a Major League Baseball investigation.

The circumstances for the probe were not yet publicly clear, but the MLB investigation is ongoing.

Eppler stepped down three days after he attended the news conference of new president of baseball operations David Stearns, a boss who said he was “looking forward to working with” Eppler.

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

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

Eppler did not immediately return messages seeking further comment.

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

“Billy Eppler led this team through a 101-win season and postseason berth last year and he will be missed,” Cohen said in the statement. “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.”

While specifics on the league’s investigation were still being sought, the GM’s resignation marked another embarrassing exit for a Mets official.

Before team president Sandy Alderson stepped aside and became a special adviser in early 2023, he helped Cohen hire Eppler and said the “vetting process was broader and deeper than any vetting process we had ever undergone” because of past mistakes.

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

In January 2021, Porter was found to have previously sexually harassed a female journalist while working for the Cubs.

Scott took over and became acting GM until September 2021, when he was arrested on drunken-driving charges for which he was later acquitted.

Before Porter and Scott there was Mickey Callaway, the Mets manager from 2018-19. 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 GM after a prolonged search for a president of baseball operations came up empty. He impressed early on and led an organization that gambled well on free agents and landed Max Scherzer, assembling an excellent team in 2022 that was knocked out in the wild-card round.

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

Eppler has been hailed particularly for his strength on the international market, having landed Shohei Ohtani when he led the Angels and Kodai Senga with the Mets. He will not be around during an offseason in which Ohtani is a free agent and Japanese righty Yoshinobu Yamamoto will hit the open market.

Virtually as soon as Eppler was hired, it was known that Cohen eventually would appoint someone above him. Publicly, Eppler had been consistently OK serving as a GM under a president of baseball operations, and as recently as Monday, the Mets spoke as if they were expecting Eppler to be a part of their future.

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

Cohen stated he wanted the front office to be as deep as possible.

“It’s my goal to build up the management talent in this organization,” Cohen said. “Baseball operations is pretty complicated. There’s a lot of moving parts. And building a strong management team is paramount to me.”