NEW YORK -- Asked this week at new president of baseball operations David Stearns’ introductory press conference about the fate of general manager Billy Eppler, who had gone from first to second on the Mets’ baseball operations hierarchy, team owner Steve Cohen indicated there was room for both men to work together in the new front office.

That vision lasted precisely three days. Eppler resigned on Thursday, the club announced, and a source later confirmed MLB is conducting an investigation regarding Eppler. That has left a sizeable hole below Stearns in baseball ops.

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

Eppler, 48, led baseball operations for less than two years upon signing a four-year contract as GM. He presided over a 101-win team in 2022, but his offseason shopping spree last winter led to a 75-win roster in ’23.

The New York Post first reported that MLB opened an investigation into Eppler's potentially improper use of the injured list, prompting his resignation. A source confirmed that MLB is investigating Eppler but not the nature of the investigation.

Before joining the Mets, Eppler served as Angels GM for five seasons and Yankees assistant GM for three.

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

Eppler’s most notable moves with the Mets included the free-agent signings of Max Scherzer, Starling Marte, Mark Canha and Eduardo Escobar his first winter, following by a record spending spree on Justin Verlander, Brandon Nimmo, Edwin Díaz, Kodai Senga and several others last offseason. Those plans included a decision to part with longtime ace Jacob deGrom.

Eppler also made many notable trades, including 2022 deals for Daniel Vogelbach and Darin Ruf, as well as a slew of Trade Deadline deals this summer that shipped out Scherzer, Verlander and others for prospects. His legacy as Mets GM will likely depend upon how well the latter trades end up for the Mets.

Eppler’s departure leaves a hole in baseball ops below Stearns, who inherits a pair of assistant GMs in Ian Levin and Ben Zauzmer -- both of whom predated Eppler in the organization -- as well as lower-ranking Eppler hires including senior vice president of baseball ops Jonathan Strangio and director of Major League ops Elizabeth Benn. Eppler had dismissed several other baseball operations employees in August, including pro scouting director Jeff Lebow and farm director Kevin Howard.

It is a departure from the vision Cohen laid out Monday when he explained why he expected Eppler to continue working as GM under Stearns.

“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. Building a strong management team is paramount. And so I viewed it as one and one equals three.”

Whatever plans Stearns has to hire or promote a GM are not yet clear. A more pressing order of business for Stearns is to find a manager after the team fired Buck Showalter last weekend. One potential candidate, Craig Counsell, was just eliminated from the playoffs in Milwaukee, making him eligible to interview for the job. Stearns has said he intends to cast a “wide net” in search of a new manager.